"ID"	"title"	"gsm"	"series_id"	"gpl"	"status"	"submission_date"	"last_update_date"	"type"	"source_name_ch1"	"organism_ch1"	"characteristics_ch1"	"molecule_ch1"	"label_ch1"	"treatment_protocol_ch1"	"extract_protocol_ch1"	"label_protocol_ch1"	"hyb_protocol"	"description"	"data_processing"	"contact"	"supplementary_file"	"data_row_count"	"channel_count"	"PuMaQC.file.gz"	"PuMaQC.file"	"PuMaQC.size.gz"	"PuMaQC.size"	"PuMaQC.code"	"PuMaQC"
158369	"Lung 3 Normal"	"GSM175977"	"GSE7307"	"GPL570"	"Public on Apr 09 2007"	"2007-03-19"	"2007-04-09"	"RNA"	"Male/Female; Normal/Diseased"	"Homo sapiens"	"Tissue/Cell Line [C]: lung;	Disease/Normal or Treatment [C]: normal;	Gender: F;	Disease type: Normal"	"total RNA"	"biotin"	"Not treated"	"Trizol extraction of total RNA was performed according to the manufacturer's instructions."	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix)."	"Following fragmentation, cRNA were hybridized for 16 hr at 45C on the GeneChip Human U133 plus 2.0 array.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Normal"	"The data were analyzed with robust multi-array (RMA) for background correction, normalization and polishing."	"Name: Richard,B,Roth;	Email: rroth@neurocrine.com;	Department: Molecular Medicine;	Institute: Neurocrine Biosciences, Inc.;	Address: 12790 El Camino Real;	City: San Diego;	State: CA;	Zip/postal_code: 92130;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM175nnn/GSM175977/GSM175977.CEL.gz"	54675	1	"download/GSM175977.CEL.gz"	"download/GSM175977.CEL"	7647904	13551305	64	1
158370	"Bronchus 2 Normal"	"GSM175978"	"GSE7307"	"GPL570"	"Public on Apr 09 2007"	"2007-03-19"	"2007-04-09"	"RNA"	"Male/Female; Normal/Diseased"	"Homo sapiens"	"Tissue/Cell Line [C]: bronchus;	Disease/Normal or Treatment [C]: normal;	Gender: M;	Disease type: Normal"	"total RNA"	"biotin"	"Not treated"	"Trizol extraction of total RNA was performed according to the manufacturer's instructions."	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix)."	"Following fragmentation, cRNA were hybridized for 16 hr at 45C on the GeneChip Human U133 plus 2.0 array.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Normal"	"The data were analyzed with robust multi-array (RMA) for background correction, normalization and polishing."	"Name: Richard,B,Roth;	Email: rroth@neurocrine.com;	Department: Molecular Medicine;	Institute: Neurocrine Biosciences, Inc.;	Address: 12790 El Camino Real;	City: San Diego;	State: CA;	Zip/postal_code: 92130;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM175nnn/GSM175978/GSM175978.CEL.gz"	54675	1	"download/GSM175978.CEL.gz"	"download/GSM175978.CEL"	7646204	13551793	64	1
158371	"Bronchus 3 Normal"	"GSM175979"	"GSE7307"	"GPL570"	"Public on Apr 09 2007"	"2007-03-19"	"2007-04-09"	"RNA"	"Male/Female; Normal/Diseased"	"Homo sapiens"	"Tissue/Cell Line [C]: bronchus;	Disease/Normal or Treatment [C]: normal;	Gender: F;	Disease type: Normal"	"total RNA"	"biotin"	"Not treated"	"Trizol extraction of total RNA was performed according to the manufacturer's instructions."	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix)."	"Following fragmentation, cRNA were hybridized for 16 hr at 45C on the GeneChip Human U133 plus 2.0 array.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Normal"	"The data were analyzed with robust multi-array (RMA) for background correction, normalization and polishing."	"Name: Richard,B,Roth;	Email: rroth@neurocrine.com;	Department: Molecular Medicine;	Institute: Neurocrine Biosciences, Inc.;	Address: 12790 El Camino Real;	City: San Diego;	State: CA;	Zip/postal_code: 92130;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM175nnn/GSM175979/GSM175979.CEL.gz"	54675	1	"download/GSM175979.CEL.gz"	"download/GSM175979.CEL"	7606765	13552025	64	1
158404	"Lung 1 Normal"	"GSM176012"	"GSE7307"	"GPL570"	"Public on Apr 09 2007"	"2007-03-19"	"2007-04-09"	"RNA"	"Male/Female; Normal/Diseased"	"Homo sapiens"	"Tissue/Cell Line [C]: lung;	Disease/Normal or Treatment [C]: normal;	Gender: M;	Disease type: Normal"	"total RNA"	"biotin"	"Not treated"	"Trizol extraction of total RNA was performed according to the manufacturer's instructions."	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix)."	"Following fragmentation, cRNA were hybridized for 16 hr at 45C on the GeneChip Human U133 plus 2.0 array.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Normal"	"The data were analyzed with robust multi-array (RMA) for background correction, normalization and polishing."	"Name: Richard,B,Roth;	Email: rroth@neurocrine.com;	Department: Molecular Medicine;	Institute: Neurocrine Biosciences, Inc.;	Address: 12790 El Camino Real;	City: San Diego;	State: CA;	Zip/postal_code: 92130;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM176nnn/GSM176012/GSM176012.CEL.gz"	54675	1	"download/GSM176012.CEL.gz"	"download/GSM176012.CEL"	7552760	13550765	64	1
158413	"Lung 4 Normal"	"GSM176021"	"GSE7307"	"GPL570"	"Public on Apr 09 2007"	"2007-03-19"	"2007-04-09"	"RNA"	"Male/Female; Normal/Diseased"	"Homo sapiens"	"Tissue/Cell Line [C]: lung;	Disease/Normal or Treatment [C]: normal;	Gender: M;	Disease type: Normal"	"total RNA"	"biotin"	"Not treated"	"Trizol extraction of total RNA was performed according to the manufacturer's instructions."	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix)."	"Following fragmentation, cRNA were hybridized for 16 hr at 45C on the GeneChip Human U133 plus 2.0 array.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Normal"	"The data were analyzed with robust multi-array (RMA) for background correction, normalization and polishing."	"Name: Richard,B,Roth;	Email: rroth@neurocrine.com;	Department: Molecular Medicine;	Institute: Neurocrine Biosciences, Inc.;	Address: 12790 El Camino Real;	City: San Diego;	State: CA;	Zip/postal_code: 92130;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM176nnn/GSM176021/GSM176021.CEL.gz"	54675	1	"download/GSM176021.CEL.gz"	"download/GSM176021.CEL"	8106318	13551808	64	1
158414	"Bronchus 4 Normal"	"GSM176022"	"GSE7307"	"GPL570"	"Public on Apr 09 2007"	"2007-03-19"	"2007-04-09"	"RNA"	"Male/Female; Normal/Diseased"	"Homo sapiens"	"Tissue/Cell Line [C]: bronchus;	Disease/Normal or Treatment [C]: normal;	Gender: M;	Disease type: Normal"	"total RNA"	"biotin"	"Not treated"	"Trizol extraction of total RNA was performed according to the manufacturer's instructions."	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix)."	"Following fragmentation, cRNA were hybridized for 16 hr at 45C on the GeneChip Human U133 plus 2.0 array.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Normal"	"The data were analyzed with robust multi-array (RMA) for background correction, normalization and polishing."	"Name: Richard,B,Roth;	Email: rroth@neurocrine.com;	Department: Molecular Medicine;	Institute: Neurocrine Biosciences, Inc.;	Address: 12790 El Camino Real;	City: San Diego;	State: CA;	Zip/postal_code: 92130;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM176nnn/GSM176022/GSM176022.CEL.gz"	54675	1	"download/GSM176022.CEL.gz"	"download/GSM176022.CEL"	8025207	13551524	64	1
197691	"NHBE siCyc 1"	"GSM219579"	"GSE8837"	"GPL570"	"Public on Aug 20 2008"	"2007-08-21"	"2007-08-22"	"RNA"	"NHBE lung cells, siCyc."	"Homo sapiens"	"Primary cell culture.;	27 year old male. "	"total RNA"	"Biotin"	"Cells were treated with siRNA oligonucleotide against Cyclophilin B for 72 hours. siRNA oligonucleotide was introduced into the cells using GeneFECTOR (Venn Nova)."	"Total RNA was extracted using the RNeasy kit from QIAGEN."	"cDNA was generated from 5 μg of total RNA by using the SuperScript Choice kit (Invitrogen)"	"Standard Affymetrix protocol"	"Data is part of NHBE siRhoBTB2 experiment."	"GC-RMA algorithm"	"Name: Harry Mellor;	Department: Department of Biochemistry;	Institute: University of Bristol;	Address: School of Medical Sciences, University Walk;	City: Bristol;	State: Avon;	Zip/postal_code: BS8 1TD;	Country: United Kingdom;	Web_link: http://www.bris.ac.uk/biochemistry/"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM219nnn/GSM219579/GSM219579.CEL.gz"	54675	1	"download/GSM219579.CEL.gz"	"download/GSM219579.CEL"	5193424	13553619	64	1
197693	"NHBE siRhoBTB2.1_rep1"	"GSM219581"	"GSE8837"	"GPL570"	"Public on Aug 20 2008"	"2007-08-21"	"2007-08-22"	"RNA"	"NHBE siRhoBTB2.1"	"Homo sapiens"	"Primary lung cell line.;	27 year old male."	"total RNA"	"Biotin"	"Cells were treated with siRNA oligonucleotide against RhoBTB2 for 72 hours. siRNA oligonucleotide was introduced into the cells using GeneFECTOR (Venn Nova)."	"Total RNA was extracted using the RNeasy kit from QIAGEN."	"cDNA was generated from 5 μg of total RNA by using the SuperScript Choice kit (Invitrogen)"	"Standard Affymetrix protocol"	"Data is part of NHBE siRhoBTB2 experiment."	"GC-RMA algorithm"	"Name: Harry Mellor;	Department: Department of Biochemistry;	Institute: University of Bristol;	Address: School of Medical Sciences, University Walk;	City: Bristol;	State: Avon;	Zip/postal_code: BS8 1TD;	Country: United Kingdom;	Web_link: http://www.bris.ac.uk/biochemistry/"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM219nnn/GSM219581/GSM219581.CEL.gz"	54675	1	"download/GSM219581.CEL.gz"	"download/GSM219581.CEL"	5026600	13551260	64	1
197694	"NHBE siCyc_rep2"	"GSM219582"	"GSE8837"	"GPL570"	"Public on Aug 20 2008"	"2007-08-21"	"2007-08-22"	"RNA"	"NHBE lung cells, siCyc"	"Homo sapiens"	"Primary cell culture. 27 year old male."	"total RNA"	"Biotin"	"Cells were treated with siRNA oligonucleotide against RhoBTB2 for 72 hours. siRNA oligonucleotide was introduced into the cells using GeneFECTOR (Venn Nova)."	"Total RNA was extracted using the RNeasy kit from QIAGEN."	"cDNA was generated from 5 μg of total RNA by using the SuperScript Choice kit (Invitrogen)"	"Standard Affymetrix protocol"	"Data is part of NHBE siRhoBTB2 experiment."	"GC-RMA algorithm"	"Name: Harry Mellor;	Department: Department of Biochemistry;	Institute: University of Bristol;	Address: School of Medical Sciences, University Walk;	City: Bristol;	State: Avon;	Zip/postal_code: BS8 1TD;	Country: United Kingdom;	Web_link: http://www.bris.ac.uk/biochemistry/"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM219nnn/GSM219582/GSM219582.CEL.gz"	54675	1	"download/GSM219582.CEL.gz"	"download/GSM219582.CEL"	4917192	13552410	64	1
197695	"NHBE siLam.1"	"GSM219583"	"GSE8837"	"GPL570"	"Public on Aug 20 2008"	"2007-08-21"	"2007-08-22"	"RNA"	"NHBE lung cells, siLam"	"Homo sapiens"	"Primary cell culture. 27 year old male."	"total RNA"	"Biotin"	"Cells were treated with siRNA oligonucleotide against RhoBTB2 for 72 hours. siRNA oligonucleotide was introduced into the cells using GeneFECTOR (Venn Nova)."	"Total RNA was extracted using the RNeasy kit from QIAGEN."	"cDNA was generated from 5 μg of total RNA by using the SuperScript Choice kit (Invitrogen)"	"Standard Affymetrix protocol"	"Data is part of NHBE siRhoBTB2 experiment."	"GC-RMA algorithm"	"Name: Harry Mellor;	Department: Department of Biochemistry;	Institute: University of Bristol;	Address: School of Medical Sciences, University Walk;	City: Bristol;	State: Avon;	Zip/postal_code: BS8 1TD;	Country: United Kingdom;	Web_link: http://www.bris.ac.uk/biochemistry/"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM219nnn/GSM219583/GSM219583.CEL.gz"	54675	1	"download/GSM219583.CEL.gz"	"download/GSM219583.CEL"	4970127	13554363	64	1
197696	"NHBE siDBC2.1_rep2"	"GSM219584"	"GSE8837"	"GPL570"	"Public on Aug 20 2008"	"2007-08-21"	"2007-08-22"	"RNA"	"NHBE lung cells, siDBC2.1"	"Homo sapiens"	"Primary cell culture. 27 year old male."	"total RNA"	"Biotin"	"Cells were treated with siRNA oligonucleotide against RhoBTB2 for 72 hours. siRNA oligonucleotide was introduced into the cells using GeneFECTOR (Venn Nova)."	"Total RNA was extracted using the RNeasy kit from QIAGEN."	"cDNA was generated from 5 μg of total RNA by using the SuperScript Choice kit (Invitrogen)"	"Standard Affymetrix protocol"	"Data is part of NHBE siRhoBTB2 experiment."	"GC-RMA algorithm"	"Name: Harry Mellor;	Department: Department of Biochemistry;	Institute: University of Bristol;	Address: School of Medical Sciences, University Walk;	City: Bristol;	State: Avon;	Zip/postal_code: BS8 1TD;	Country: United Kingdom;	Web_link: http://www.bris.ac.uk/biochemistry/"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM219nnn/GSM219584/GSM219584.CEL.gz"	54675	1	"download/GSM219584.CEL.gz"	"download/GSM219584.CEL"	5002746	13552256	64	1
197697	"NHBE siRhoBTB2.2"	"GSM219585"	"GSE8837"	"GPL570"	"Public on Aug 20 2008"	"2007-08-21"	"2007-08-22"	"RNA"	"NHBE lung cells, siRhoBTB2.2"	"Homo sapiens"	"Primary cell culture. 27 year old male."	"total RNA"	"Biotin"	"Cells were treated with siRNA oligonucleotide against RhoBTB2 for 72 hours. siRNA oligonucleotide was introduced into the cells using GeneFECTOR (Venn Nova)."	"Total RNA was extracted using the RNeasy kit from QIAGEN."	"cDNA was generated from 5 μg of total RNA by using the SuperScript Choice kit (Invitrogen)"	"Standard Affymetrix protocol"	"Data is part of NHBE siRhoBTB2 experiment."	"GC-RMA algorithm"	"Name: Harry Mellor;	Department: Department of Biochemistry;	Institute: University of Bristol;	Address: School of Medical Sciences, University Walk;	City: Bristol;	State: Avon;	Zip/postal_code: BS8 1TD;	Country: United Kingdom;	Web_link: http://www.bris.ac.uk/biochemistry/"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM219nnn/GSM219585/GSM219585.CEL.gz"	54675	1	"download/GSM219585.CEL.gz"	"download/GSM219585.CEL"	5030081	13552032	64	1
197698	"NHBE siCYC_rep3"	"GSM219586"	"GSE8837"	"GPL570"	"Public on Aug 20 2008"	"2007-08-21"	"2007-08-22"	"RNA"	"NHBE lung cells, siCyc."	"Homo sapiens"	"Primary cell culture 27 year old male."	"total RNA"	"Biotin"	"Cells were treated with siRNA oligonucleotide against RhoBTB2 for 72 hours. siRNA oligonucleotide was introduced into the cells using GeneFECTOR (Venn Nova)."	"Total RNA was extracted using the RNeasy kit from QIAGEN."	"cDNA was generated from 5 μg of total RNA by using the SuperScript Choice kit (Invitrogen)"	"Standard Affymetrix protocol"	"Data is part of NHBE siRhoBTB2 experiment."	"GC-RMA algorithm"	"Name: Harry Mellor;	Department: Department of Biochemistry;	Institute: University of Bristol;	Address: School of Medical Sciences, University Walk;	City: Bristol;	State: Avon;	Zip/postal_code: BS8 1TD;	Country: United Kingdom;	Web_link: http://www.bris.ac.uk/biochemistry/"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM219nnn/GSM219586/GSM219586.CEL.gz"	54675	1	"download/GSM219586.CEL.gz"	"download/GSM219586.CEL"	5032503	13551834	64	1
197699	"NHBE siLam_rep2"	"GSM219587"	"GSE8837"	"GPL570"	"Public on Aug 20 2008"	"2007-08-21"	"2007-08-22"	"RNA"	"NHBE lung cells, siLam"	"Homo sapiens"	"Primary cell culture. 27 year old male."	"total RNA"	"Biotin"	"Cells were treated with siRNA oligonucleotide against RhoBTB2 for 72 hours. siRNA oligonucleotide was introduced into the cells using GeneFECTOR (Venn Nova)."	"Total RNA was extracted using the RNeasy kit from QIAGEN."	"cDNA was generated from 5 μg of total RNA by using the SuperScript Choice kit (Invitrogen)"	"Standard Affymetrix protocol"	"Data is part of NHBE siRhoBTB2 experiment."	"GC-RMA algorithm"	"Name: Harry Mellor;	Department: Department of Biochemistry;	Institute: University of Bristol;	Address: School of Medical Sciences, University Walk;	City: Bristol;	State: Avon;	Zip/postal_code: BS8 1TD;	Country: United Kingdom;	Web_link: http://www.bris.ac.uk/biochemistry/"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM219nnn/GSM219587/GSM219587.CEL.gz"	54675	1	"download/GSM219587.CEL.gz"	"download/GSM219587.CEL"	5047636	13551527	64	1
197701	"NHBE siRhoBTB2.1_rep3"	"GSM219589"	"GSE8837"	"GPL570"	"Public on Aug 20 2008"	"2007-08-21"	"2007-08-22"	"RNA"	"NHBE lung cells, siRhoBTB2.1"	"Homo sapiens"	"Primary cell culture. 27 year old male."	"total RNA"	"Biotin"	"Cells were treated with siRNA oligonucleotide against RhoBTB2 for 72 hours. siRNA oligonucleotide was introduced into the cells using GeneFECTOR (Venn Nova)."	"Total RNA was extracted using the RNeasy kit from QIAGEN."	"cDNA was generated from 5 μg of total RNA by using the SuperScript Choice kit (Invitrogen)"	"Standard Affymetrix protocol"	"Data is part of NHBE siRhoBTB2 experiment."	"GC-RMA algorithm"	"Name: Harry Mellor;	Department: Department of Biochemistry;	Institute: University of Bristol;	Address: School of Medical Sciences, University Walk;	City: Bristol;	State: Avon;	Zip/postal_code: BS8 1TD;	Country: United Kingdom;	Web_link: http://www.bris.ac.uk/biochemistry/"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM219nnn/GSM219589/GSM219589.CEL.gz"	54675	1	"download/GSM219589.CEL.gz"	"download/GSM219589.CEL"	4875808	13551392	64	1
197702	"NHBE siRhoBTB2.2_rep2"	"GSM219590"	"GSE8837"	"GPL570"	"Public on Aug 20 2008"	"2007-08-21"	"2007-08-22"	"RNA"	"NHBE lung cells, siRhoBTB2.2"	"Homo sapiens"	"Primary cell culture. 27 year old male."	"total RNA"	"Biotin"	"Cells were treated with siRNA oligonucleotide against RhoBTB2 for 72 hours. siRNA oligonucleotide was introduced into the cells using GeneFECTOR (Venn Nova)."	"Total RNA was extracted using the RNeasy kit from QIAGEN."	"cDNA was generated from 5 μg of total RNA by using the SuperScript Choice kit (Invitrogen)"	"Standard Affymetrix protocol"	"Data is part of NHBE siRhoBTB2 experiment."	"GC-RMA algorithm"	"Name: Harry Mellor;	Department: Department of Biochemistry;	Institute: University of Bristol;	Address: School of Medical Sciences, University Walk;	City: Bristol;	State: Avon;	Zip/postal_code: BS8 1TD;	Country: United Kingdom;	Web_link: http://www.bris.ac.uk/biochemistry/"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM219nnn/GSM219590/GSM219590.CEL.gz"	54675	1	"download/GSM219590.CEL.gz"	"download/GSM219590.CEL"	4914759	13551441	64	1
255680	"Control (Control106) Contractile Heavy polyribosomal RNA"	"GSM281952"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"other"	"Control106"	"Homo sapiens"	"Lung myofibroblasts;	Control;	Contractile Heavy polyribosomal RNA"	"other"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281952/GSM281952.CEL.gz"	26714	1	"download/GSM281952.CEL.gz"	"download/GSM281952.CEL"	8455370	13553495	64	1
255681	"Control (Control106) Contractile Total RNA"	"GSM281953"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"RNA"	"Control106"	"Homo sapiens"	"Lung myofibroblasts;	Control;	Contractile"	"total RNA"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281953/GSM281953.CEL.gz"	26714	1	"download/GSM281953.CEL.gz"	"download/GSM281953.CEL"	8087528	13552016	64	1
255682	"Control (Control128) Contractile Heavy polyribosomal RNA"	"GSM281954"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"other"	"Control128"	"Homo sapiens"	"Lung myofibroblasts;	Control;	Contractile Heavy polyribosomal RNA"	"other"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281954/GSM281954.CEL.gz"	26714	1	"download/GSM281954.CEL.gz"	"download/GSM281954.CEL"	8257138	13552286	64	1
255683	"Control (Control128) Contractile Total RNA"	"GSM281955"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"RNA"	"Control128"	"Homo sapiens"	"Lung myofibroblasts;	Control;	Contractile"	"total RNA"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281955/GSM281955.CEL.gz"	26714	1	"download/GSM281955.CEL.gz"	"download/GSM281955.CEL"	8202706	13551522	64	1
255684	"Control (Control54) Contractile Heavy polyribosomal RNA"	"GSM281956"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"other"	"Control54"	"Homo sapiens"	"Lung myofibroblasts;	Control;	Contractile Heavy polyribosomal RNA"	"other"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281956/GSM281956.CEL.gz"	26714	1	"download/GSM281956.CEL.gz"	"download/GSM281956.CEL"	8130993	13551568	64	1
255685	"Control (Control54) Contractile Total RNA"	"GSM281957"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"RNA"	"Control54"	"Homo sapiens"	"Lung myofibroblasts;	Control;	Contractile"	"total RNA"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281957/GSM281957.CEL.gz"	26714	1	"download/GSM281957.CEL.gz"	"download/GSM281957.CEL"	8440793	13551414	64	1
255686	"Control (Control57) Contractile Heavy polyribosomal RNA"	"GSM281958"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"other"	"Control57"	"Homo sapiens"	"Lung myofibroblasts;	Control;	Contractile Heavy polyribosomal RNA"	"other"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281958/GSM281958.CEL.gz"	26714	1	"download/GSM281958.CEL.gz"	"download/GSM281958.CEL"	7882533	13553539	64	1
255687	"Control (Control57) Contractile Total RNA"	"GSM281959"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"RNA"	"Control57"	"Homo sapiens"	"Lung myofibroblasts;	Control;	Contractile"	"total RNA"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281959/GSM281959.CEL.gz"	26714	1	"download/GSM281959.CEL.gz"	"download/GSM281959.CEL"	8185862	13551156	64	1
255688	"Control (Control78) Contractile Heavy polyribosomal RNA"	"GSM281960"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"other"	"Control78"	"Homo sapiens"	"Lung myofibroblasts;	Control;	Contractile Heavy polyribosomal RNA"	"other"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281960/GSM281960.CEL.gz"	26714	1	"download/GSM281960.CEL.gz"	"download/GSM281960.CEL"	8115858	13551572	64	1
255689	"Control (Control78) Contractile Total RNA"	"GSM281961"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"RNA"	"Control78"	"Homo sapiens"	"Lung myofibroblasts;	Control;	Contractile"	"total RNA"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281961/GSM281961.CEL.gz"	26714	1	"download/GSM281961.CEL.gz"	"download/GSM281961.CEL"	8207190	13552228	64	1
255690	"Control (Control89) Contractile Heavy polyribosomal RNA"	"GSM281962"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"other"	"Control89"	"Homo sapiens"	"Lung myofibroblasts;	Control;	Contractile Heavy polyribosomal RNA"	"other"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281962/GSM281962.CEL.gz"	26714	1	"download/GSM281962.CEL.gz"	"download/GSM281962.CEL"	8164480	13551788	64	1
255691	"Control (Control89) Contractile Total RNA"	"GSM281963"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"RNA"	"Control89"	"Homo sapiens"	"Lung myofibroblasts;	Control;	Contractile"	"total RNA"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281963/GSM281963.CEL.gz"	26714	1	"download/GSM281963.CEL.gz"	"download/GSM281963.CEL"	8443665	13550452	64	1
255692	"IPF (IPF12) Contractile Heavy polyribosomal RNA"	"GSM281964"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"other"	"IPF12"	"Homo sapiens"	"Lung myofibroblasts;	IPF;	Contractile Heavy polyribosomal RNA"	"other"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281964/GSM281964.CEL.gz"	26714	1	"download/GSM281964.CEL.gz"	"download/GSM281964.CEL"	8313445	13551157	64	1
255693	"IPF (IPF12) Contractile Total RNA"	"GSM281965"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"RNA"	"IPF12"	"Homo sapiens"	"Lung myofibroblasts;	IPF;	Contractile"	"total RNA"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281965/GSM281965.CEL.gz"	26714	1	"download/GSM281965.CEL.gz"	"download/GSM281965.CEL"	8494516	13550843	64	1
255694	"IPF (IPF129) Contractile Heavy polyribosomal RNA"	"GSM281966"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"other"	"IPF129"	"Homo sapiens"	"Lung myofibroblasts;	IPF;	Contractile Heavy polyribosomal RNA"	"other"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281966/GSM281966.CEL.gz"	26714	1	"download/GSM281966.CEL.gz"	"download/GSM281966.CEL"	8028787	13552480	64	1
255695	"IPF (IPF129) Contractile Total RNA"	"GSM281967"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"RNA"	"IPF129"	"Homo sapiens"	"Lung myofibroblasts;	IPF;	Contractile"	"total RNA"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281967/GSM281967.CEL.gz"	26714	1	"download/GSM281967.CEL.gz"	"download/GSM281967.CEL"	8104373	13551864	64	1
255696	"IPF (IPF13) Contractile Heavy polyribosomal RNA"	"GSM281968"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"other"	"IPF13"	"Homo sapiens"	"Lung myofibroblasts;	IPF;	Contractile Heavy polyribosomal RNA"	"other"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281968/GSM281968.CEL.gz"	26714	1	"download/GSM281968.CEL.gz"	"download/GSM281968.CEL"	7906789	13552623	64	1
255697	"IPF (IPF13) Contractile Total RNA"	"GSM281969"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"RNA"	"IPF13"	"Homo sapiens"	"Lung myofibroblasts;	IPF;	Contractile"	"total RNA"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281969/GSM281969.CEL.gz"	26714	1	"download/GSM281969.CEL.gz"	"download/GSM281969.CEL"	8203582	13551407	64	1
255698	"IPF (IPF14) Contractile Heavy polyribosomal RNA"	"GSM281970"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"other"	"IPF14"	"Homo sapiens"	"Lung myofibroblasts;	IPF;	Contractile Heavy polyribosomal RNA"	"other"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281970/GSM281970.CEL.gz"	26714	1	"download/GSM281970.CEL.gz"	"download/GSM281970.CEL"	8198725	13551156	64	1
255699	"IPF (IPF14) Contractile Total RNA"	"GSM281971"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"RNA"	"IPF14"	"Homo sapiens"	"Lung myofibroblasts;	IPF;	Contractile"	"total RNA"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281971/GSM281971.CEL.gz"	26714	1	"download/GSM281971.CEL.gz"	"download/GSM281971.CEL"	8671191	13550489	64	1
255700	"IPF (IPF37) Contractile Heavy polyribosomal RNA"	"GSM281972"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"other"	"IPF37"	"Homo sapiens"	"Lung myofibroblasts;	IPF;	Contractile Heavy polyribosomal RNA"	"other"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281972/GSM281972.CEL.gz"	26714	1	"download/GSM281972.CEL.gz"	"download/GSM281972.CEL"	8396905	13550969	64	1
255701	"IPF (IPF37) Contractile Total RNA"	"GSM281973"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"RNA"	"IPF37"	"Homo sapiens"	"Lung myofibroblasts;	IPF;	Contractile"	"total RNA"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281973/GSM281973.CEL.gz"	26714	1	"download/GSM281973.CEL.gz"	"download/GSM281973.CEL"	8407005	13550537	64	1
255702	"IPF (IPF75) Contractile Heavy polyribosomal RNA"	"GSM281974"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"other"	"IPF75"	"Homo sapiens"	"Lung myofibroblasts;	IPF;	Contractile Heavy polyribosomal RNA"	"other"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281974/GSM281974.CEL.gz"	26714	1	"download/GSM281974.CEL.gz"	"download/GSM281974.CEL"	8223071	13551586	64	1
255703	"IPF (IPF75) Contractile Total RNA"	"GSM281975"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"RNA"	"IPF75"	"Homo sapiens"	"Lung myofibroblasts;	IPF;	Contractile"	"total RNA"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281975/GSM281975.CEL.gz"	26714	1	"download/GSM281975.CEL.gz"	"download/GSM281975.CEL"	8079223	13551704	64	1
255704	"Control (Control106) Non-contractile Heavy polyribosomal RNA"	"GSM281976"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"other"	"Control106"	"Homo sapiens"	"Lung myofibroblasts;	Control;	Non-contractile Heavy polyribosomal RNA"	"other"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281976/GSM281976.CEL.gz"	26714	1	"download/GSM281976.CEL.gz"	"download/GSM281976.CEL"	8055994	13552004	64	1
255705	"Control (Control106) Non-contractile Total RNA"	"GSM281977"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"RNA"	"Control106"	"Homo sapiens"	"Lung myofibroblasts;	Control;	Non-contractile"	"total RNA"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281977/GSM281977.CEL.gz"	26714	1	"download/GSM281977.CEL.gz"	"download/GSM281977.CEL"	8114300	13551683	64	1
255706	"Control (Control128) Non-contractile Heavy polyribosomal RNA"	"GSM281978"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"other"	"Control128"	"Homo sapiens"	"Lung myofibroblasts;	Control;	Non-contractile Heavy polyribosomal RNA"	"other"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281978/GSM281978.CEL.gz"	26714	1	"download/GSM281978.CEL.gz"	"download/GSM281978.CEL"	8098476	13551907	64	1
255707	"Control (Control128) Non-contractile Total RNA"	"GSM281979"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"RNA"	"Control128"	"Homo sapiens"	"Lung myofibroblasts;	Control;	Non-contractile"	"total RNA"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281979/GSM281979.CEL.gz"	26714	1	"download/GSM281979.CEL.gz"	"download/GSM281979.CEL"	8098667	13551852	64	1
255708	"Control (Control54) Non-contractile Heavy polyribosomal RNA"	"GSM281980"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"other"	"Control54"	"Homo sapiens"	"Lung myofibroblasts;	Control;	Non-contractile Heavy polyribosomal RNA"	"other"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281980/GSM281980.CEL.gz"	26714	1	"download/GSM281980.CEL.gz"	"download/GSM281980.CEL"	8163764	13551627	64	1
255709	"Control (Control54) Non-contractile Total RNA"	"GSM281981"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"RNA"	"Control54"	"Homo sapiens"	"Lung myofibroblasts;	Control;	Non-contractile"	"total RNA"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281981/GSM281981.CEL.gz"	26714	1	"download/GSM281981.CEL.gz"	"download/GSM281981.CEL"	8198416	13551203	64	1
255710	"Control (Control57) Non-contractile Heavy polyribosomal RNA"	"GSM281982"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"other"	"Control57"	"Homo sapiens"	"Lung myofibroblasts;	Control;	Non-contractile Heavy polyribosomal RNA"	"other"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281982/GSM281982.CEL.gz"	26714	1	"download/GSM281982.CEL.gz"	"download/GSM281982.CEL"	8212793	13551256	64	1
255711	"Control (Control57) Non-contractile Total RNA"	"GSM281983"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"RNA"	"Control57"	"Homo sapiens"	"Lung myofibroblasts;	Control;	Non-contractile"	"total RNA"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281983/GSM281983.CEL.gz"	26714	1	"download/GSM281983.CEL.gz"	"download/GSM281983.CEL"	8095063	13551056	64	1
255712	"Control (Control78) Non-contractile Heavy polyribosomal RNA"	"GSM281984"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"other"	"Control78"	"Homo sapiens"	"Lung myofibroblasts;	Control;	Non-contractile Heavy polyribosomal RNA"	"other"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281984/GSM281984.CEL.gz"	26714	1	"download/GSM281984.CEL.gz"	"download/GSM281984.CEL"	8145196	13551600	64	1
255713	"Control (Control78) Non-contractile Total RNA"	"GSM281985"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"RNA"	"Control78"	"Homo sapiens"	"Lung myofibroblasts;	Control;	Non-contractile"	"total RNA"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281985/GSM281985.CEL.gz"	26714	1	"download/GSM281985.CEL.gz"	"download/GSM281985.CEL"	8305884	13551068	64	1
255714	"Control (Control89) Non-contractile Heavy polyribosomal RNA"	"GSM281986"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"other"	"Control89"	"Homo sapiens"	"Lung myofibroblasts;	Control;	Non-contractile Heavy polyribosomal RNA"	"other"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281986/GSM281986.CEL.gz"	26714	1	"download/GSM281986.CEL.gz"	"download/GSM281986.CEL"	8318965	13551200	64	1
255715	"Control (Control89) Non-contractile Total RNA"	"GSM281987"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"RNA"	"Control89"	"Homo sapiens"	"Lung myofibroblasts;	Control;	Non-contractile"	"total RNA"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281987/GSM281987.CEL.gz"	26714	1	"download/GSM281987.CEL.gz"	"download/GSM281987.CEL"	8210523	13551087	64	1
255716	"IPF (IPF12) Non-contractile Heavy polyribosomal RNA"	"GSM281988"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"other"	"IPF12"	"Homo sapiens"	"Lung myofibroblasts;	IPF;	Non-contractile Heavy polyribosomal RNA"	"other"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281988/GSM281988.CEL.gz"	26714	1	"download/GSM281988.CEL.gz"	"download/GSM281988.CEL"	7988834	13551729	64	1
255717	"IPF (IPF12) Non-contractile Total RNA"	"GSM281989"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"RNA"	"IPF12"	"Homo sapiens"	"Lung myofibroblasts;	IPF;	Non-contractile"	"total RNA"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281989/GSM281989.CEL.gz"	26714	1	"download/GSM281989.CEL.gz"	"download/GSM281989.CEL"	8343020	13550915	64	1
255718	"IPF (IPF129) Non-contractile Heavy polyribosomal RNA"	"GSM281990"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"other"	"IPF129"	"Homo sapiens"	"Lung myofibroblasts;	IPF;	Non-contractile Heavy polyribosomal RNA"	"other"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281990/GSM281990.CEL.gz"	26714	1	"download/GSM281990.CEL.gz"	"download/GSM281990.CEL"	8162814	13552171	64	1
255719	"IPF (IPF129) Non-contractile Total RNA"	"GSM281991"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"RNA"	"IPF129"	"Homo sapiens"	"Lung myofibroblasts;	IPF;	Non-contractile"	"total RNA"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281991/GSM281991.CEL.gz"	26714	1	"download/GSM281991.CEL.gz"	"download/GSM281991.CEL"	8136502	13552022	64	1
255720	"IPF (IPF13) Non-contractile Heavy polyribosomal RNA"	"GSM281992"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"other"	"IPF13"	"Homo sapiens"	"Lung myofibroblasts;	IPF;	Non-contractile Heavy polyribosomal RNA"	"other"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281992/GSM281992.CEL.gz"	26714	1	"download/GSM281992.CEL.gz"	"download/GSM281992.CEL"	7899049	13552599	64	1
255721	"IPF (IPF13) Non-contractile Total RNA"	"GSM281993"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"RNA"	"IPF13"	"Homo sapiens"	"Lung myofibroblasts;	IPF;	Non-contractile"	"total RNA"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281993/GSM281993.CEL.gz"	26714	1	"download/GSM281993.CEL.gz"	"download/GSM281993.CEL"	8270644	13551735	64	1
255722	"IPF (IPF14) Non-contractile Heavy polyribosomal RNA"	"GSM281994"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"other"	"IPF14"	"Homo sapiens"	"Lung myofibroblasts;	IPF;	Non-contractile Heavy polyribosomal RNA"	"other"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281994/GSM281994.CEL.gz"	26714	1	"download/GSM281994.CEL.gz"	"download/GSM281994.CEL"	8106832	13551838	64	1
255723	"IPF (IPF14) Non-contractile Total RNA"	"GSM281995"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"RNA"	"IPF14"	"Homo sapiens"	"Lung myofibroblasts;	IPF;	Non-contractile"	"total RNA"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281995/GSM281995.CEL.gz"	26714	1	"download/GSM281995.CEL.gz"	"download/GSM281995.CEL"	8139631	13551411	64	1
255724	"IPF (IPF37) Non-contractile Heavy polyribosomal RNA"	"GSM281996"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"other"	"IPF37"	"Homo sapiens"	"Lung myofibroblasts;	IPF;	Non-contractile Heavy polyribosomal RNA"	"other"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281996/GSM281996.CEL.gz"	26714	1	"download/GSM281996.CEL.gz"	"download/GSM281996.CEL"	8256145	13551296	64	1
255725	"IPF (IPF37) Non-contractile Total RNA"	"GSM281997"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"RNA"	"IPF37"	"Homo sapiens"	"Lung myofibroblasts;	IPF;	Non-contractile"	"total RNA"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281997/GSM281997.CEL.gz"	26714	1	"download/GSM281997.CEL.gz"	"download/GSM281997.CEL"	8344354	13550509	64	1
255726	"IPF (IPF75) Non-contractile Heavy polyribosomal RNA"	"GSM281998"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"other"	"IPF75"	"Homo sapiens"	"Lung myofibroblasts;	IPF;	Non-contractile Heavy polyribosomal RNA"	"other"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281998/GSM281998.CEL.gz"	26714	1	"download/GSM281998.CEL.gz"	"download/GSM281998.CEL"	8257114	13551690	64	1
255727	"IPF (IPF75) Non-contractile Total RNA"	"GSM281999"	"GSE11196"	"GPL6732"	"Public on Nov 21 2008"	"2008-04-16"	"2008-11-21"	"RNA"	"IPF75"	"Homo sapiens"	"Lung myofibroblasts;	IPF;	Non-contractile"	"total RNA"	"Biotin"	"Collagen was obtained from Cohesion Corporation, Palo Alto, CA. Cells were removed from tissue culture plates using trypsin and mixed with DMEM, 10% FBS and collagen (final collagen concentration 0.5 mg/ml). This mixture was polymerized in a water bath at 37° C, aliquoted into 3.5 cm tissue culture dishes, and placed into an incubator at 37º until harvest. Final cell density was approximately 200,000 cells/ml. Tissue culture plates for non-contractile gels had been pre-coated with collagen 100 μg/ml in phosphate-buffered saline (PBS) in order to prevent matrix contraction. Cells in these non-contractile collagen matrices were incubated at 37ºC for 6 hours. Contractile matrices were prepared as above; they were allowed to polymerize in uncoated tissue culture dishes for two hours, and then the gel was released by tapping the side of the dish. They were placed in an incubator for four more hours before harvesting (for a total 6-hour incubation time, equal to non-contractile matrices). Degree of collagen matrix contraction was not significantly different between IPF and control myofibroblasts."	"Cells were harvested in log phase using trypsin and incorporated into collagen gels as described above. Myofibroblasts were collected from the gels at the predetermined time point using collagenase 5 mg/ml (Sigma, St. Louis, MO) containing cycloheximide (100 μg/ml) and collected by centrifugation. A small portion of non-homogenized cells was retained for Trireagent (Sigma) processing to isolate total cellular RNA (designated “total RNA”) for microarray analysis.  The remaining cells were used for polyribosome preparations as described (Larsson, O., Perlman, D. et al. Nucleic Acids Research 2006). Ten 0.5 ml fractions were collected from each sample into tubes containing 50 μl of 10% SDS. RNA from each fraction was processed using Trireagent according to the manufacturer’s directions and precipitated with isopropanol. Fractions 7-10, consisting of mRNA with four or more bound ribosomes, designated ”heavy” were pooled for microarray analysis."	"Biotinylated cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10 ug RNA"	"Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450."	"Comparison of lung myofibroblasts from patients with Idiopatic Pulmonary Fibrosis (IPF, 6 donors) to control (6 donors) in contractile and non-contractile matrices using both total and polyribosomal RNA."	"The data was normalized using GCRMA and updated probe sets definitions “RefSeq v7” as defined in GPL6732."	"Name: Ola Larsson;	Email: ola.larsson@mail.mcgill.ca;	Phone: + 1 514 398  4400 ext 09257;	Department: Department of Biochemistry;	Institute: McGill Univeristy;	Address: 1160 Pine Avenue West;	City: Montreal;	State: QC;	Zip/postal_code: H3A1A3;	Country: Canada"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM281nnn/GSM281999/GSM281999.CEL.gz"	26714	1	"download/GSM281999.CEL.gz"	"download/GSM281999.CEL"	8150970	13551500	64	1
276582	"human reference, biological rep1"	"GSM304263"	"GSE12034"	"GPL570"	"Public on Jul 09 2008"	"2008-07-08"	"2008-07-14"	"RNA"	"Pool of ten normal human tissues for reference"	"Homo sapiens"	"Genotype: 10 different normal human tissues, including skeletal muscle, kidney, lung, colon, liver, spleen, breast, brain, heart, and stomach.;	Age: N/A"	"total RNA"	"biotin"	"Samples are obtained from Ambion"	"The samples are processed using Ambion's RNA isolation reagents to produce highly pure, intact RNA. A stringent DNase treatment is performed to ensure that the RNA is ready for use in any downstream application, including RT-PCR."	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix)."	"Hybridization cocktails of 300 ml containing 15 mg of fragmented biotin-labeled aRNA and biotinylated exogenous hybridization controls (50 pM control Oligo B2, Eukaryotic hybridization controls) (BioB at 1.5 pM, BioC at 5 pM, BioD at 25 pM, and CreX at 100 pM), herring sperm DNA (0.1 mg/ml), BSA (0.5 mg/ml) in buffer (100 mM Mes/1M NaCl/20 mM EDTA/0.01% Tween 20) were hybridized to the GeneChip Human Genome U133 plus 2.0 array (Affymetrix, Santa Clara, CA). Hybridizations were performed automatically, and each array was prehybridized with all components except the fragmented biotin-labeled aRNA in a chamber at 45°C for 15 min with rotation at 60 rpm. The prehybridized array was then hybridized with the aRNA mixture for 16 h under the prehybridization conditions."	"Gene expression data from pool of 10 normal human tissue."	"The data were analyzed with dChip using smoothing spline invariant set method with the model based expression algorithm following the perfect match (PM)-mismatch (MM) difference model. In the dChip analysis, array outliers are not treated as missing expression values and no truncation on signal values is applied."	"Name: Arif,Murat,Kocabas;	Email: kocabas@msu.edu, hotu@bidmc.harvard.edu;	Phone: 517-432-8254;	Fax: 517-432-8742;	Laboratory: Cellular Reprogramming Laboratory;	Department: Animal Science;	Institute: Michigan State University;	Address: B270 Anthony Hall;	City: East Lansing;	State: MI;	Zip/postal_code: 48824;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM304nnn/GSM304263/GSM304263.CEL.gz"	54675	1	"download/GSM304263.CEL.gz"	"download/GSM304263.CEL"	5027108	13554224	64	1
276583	"human reference, biological rep2"	"GSM304264"	"GSE12034"	"GPL570"	"Public on Jul 09 2008"	"2008-07-08"	"2008-07-14"	"RNA"	"Pool of ten normal human tissues for reference"	"Homo sapiens"	"Genotype: 10 different normal human tissues, including skeletal muscle, kidney, lung, colon, liver, spleen, breast, brain, heart, and stomach.;	Age: N/A"	"total RNA"	"biotin"	"Samples are obtained from Ambion"	"The samples are processed using Ambion's RNA isolation reagents to produce highly pure, intact RNA. A stringent DNase treatment is performed to ensure that the RNA is ready for use in any downstream application, including RT-PCR."	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix)."	"Hybridization cocktails of 300 ml containing 15 mg of fragmented biotin-labeled aRNA and biotinylated exogenous hybridization controls (50 pM control Oligo B2, Eukaryotic hybridization controls) (BioB at 1.5 pM, BioC at 5 pM, BioD at 25 pM, and CreX at 100 pM), herring sperm DNA (0.1 mg/ml), BSA (0.5 mg/ml) in buffer (100 mM Mes/1M NaCl/20 mM EDTA/0.01% Tween 20) were hybridized to the GeneChip Human Genome U133 plus 2.0 array (Affymetrix, Santa Clara, CA). Hybridizations were performed automatically, and each array was prehybridized with all components except the fragmented biotin-labeled aRNA in a chamber at 45°C for 15 min with rotation at 60 rpm. The prehybridized array was then hybridized with the aRNA mixture for 16 h under the prehybridization conditions."	"Gene expression data from pool of 10 normal human tissue."	"The data were analyzed with dChip using smoothing spline invariant set method with the model based expression algorithm following the perfect match (PM)-mismatch (MM) difference model. In the dChip analysis, array outliers are not treated as missing expression values and no truncation on signal values is applied."	"Name: Arif,Murat,Kocabas;	Email: kocabas@msu.edu, hotu@bidmc.harvard.edu;	Phone: 517-432-8254;	Fax: 517-432-8742;	Laboratory: Cellular Reprogramming Laboratory;	Department: Animal Science;	Institute: Michigan State University;	Address: B270 Anthony Hall;	City: East Lansing;	State: MI;	Zip/postal_code: 48824;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM304nnn/GSM304264/GSM304264.CEL.gz"	54675	1	"download/GSM304264.CEL.gz"	"download/GSM304264.CEL"	4757374	13567729	64	1
276584	"human reference, biological rep3"	"GSM304265"	"GSE12034"	"GPL570"	"Public on Jul 09 2008"	"2008-07-08"	"2008-07-14"	"RNA"	"Pool of ten normal human tissues for reference"	"Homo sapiens"	"Genotype: 10 different normal human tissues, including skeletal muscle, kidney, lung, colon, liver, spleen, breast, brain, heart, and stomach.;	Age: N/A"	"total RNA"	"biotin"	"Samples are obtained from Ambion"	"The samples are processed using Ambion's RNA isolation reagents to produce highly pure, intact RNA. A stringent DNase treatment is performed to ensure that the RNA is ready for use in any downstream application, including RT-PCR."	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix)."	"Hybridization cocktails of 300 ml containing 15 mg of fragmented biotin-labeled aRNA and biotinylated exogenous hybridization controls (50 pM control Oligo B2, Eukaryotic hybridization controls) (BioB at 1.5 pM, BioC at 5 pM, BioD at 25 pM, and CreX at 100 pM), herring sperm DNA (0.1 mg/ml), BSA (0.5 mg/ml) in buffer (100 mM Mes/1M NaCl/20 mM EDTA/0.01% Tween 20) were hybridized to the GeneChip Human Genome U133 plus 2.0 array (Affymetrix, Santa Clara, CA). Hybridizations were performed automatically, and each array was prehybridized with all components except the fragmented biotin-labeled aRNA in a chamber at 45°C for 15 min with rotation at 60 rpm. The prehybridized array was then hybridized with the aRNA mixture for 16 h under the prehybridization conditions."	"Gene expression data from pool of 10 normal human tissue."	"The data were analyzed with dChip using smoothing spline invariant set method with the model based expression algorithm following the perfect match (PM)-mismatch (MM) difference model. In the dChip analysis, array outliers are not treated as missing expression values and no truncation on signal values is applied."	"Name: Arif,Murat,Kocabas;	Email: kocabas@msu.edu, hotu@bidmc.harvard.edu;	Phone: 517-432-8254;	Fax: 517-432-8742;	Laboratory: Cellular Reprogramming Laboratory;	Department: Animal Science;	Institute: Michigan State University;	Address: B270 Anthony Hall;	City: East Lansing;	State: MI;	Zip/postal_code: 48824;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM304nnn/GSM304265/GSM304265.CEL.gz"	54675	1	"download/GSM304265.CEL.gz"	"download/GSM304265.CEL"	4968362	13590596	64	1
279210	"HLF 1-1 (No)"	"GSM307029"	"GSE12205"	"GPL570"	"Public on Dec 02 2008"	"2008-07-22"	"2008-12-02"	"RNA"	"Human lung fibroblasts"	"Homo sapiens"	"Normal diploid human lung fibroblast cell line, LL24, was originally isolated from normal autopsy tissue of an 11-year-old male."	"total RNA"	"biotin"	"culture medium for 24hr"	"Following 24hr treatment with culture medium, RNA was isolated using RNA-Bee (Tel-Test, Friendswood, TX) followed by a secondary purification on Qiagen RNAeasy Mini columns (Qiagen, Valencia, CA). RNA quality was assessed by Agilent bioanalyzer and RNA Integrity Numbers (RIN) for samples were >9.9."	"Total RNA (10 ug) was labeled by One-Cycle Target Labeling Kit as specified by Affymetrix."	"Hybridization, washing and staining were carried out according to the Affymetrix’s instructions."	"no additional information"	"Default normalization steps recommended by GeneSpring software were used:;	(1) data transformation: set measurements less than 0.01 to 0.01;	(2) per chip: normalize to 50th percentile;	(3) per gene: normalize to median"	"Name: DONG-SOON BAE;	Email: phmdxb@gwumc.edu;	Phone: 202-994-0964;	Fax: 202-994-2870;	Department: Pharmacology & Physiology;	Institute: George Washinton Uni.;	Address: 2300 I Street, NW;	City: Washington;	State: DC;	Zip/postal_code: 20037;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM307nnn/GSM307029/GSM307029.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM307nnn/GSM307029/GSM307029.CHP.gz"	54675	1	"download/GSM307029.CEL.gz"	"download/GSM307029.CEL"	5215512	13550605	64	1
279214	"HLF 1-2 (No)"	"GSM307033"	"GSE12205"	"GPL570"	"Public on Dec 02 2008"	"2008-07-22"	"2008-12-02"	"RNA"	"Human lung fibroblats"	"Homo sapiens"	"Normal diploid human lung fibroblast cell line, LL24, was originally isolated from normal autopsy tissue of an 11-year-old male."	"total RNA"	"biotin"	"culture medium for 24hr"	"Following 24hr treatment with culture medium, RNA was isolated using RNA-Bee (Tel-Test, Friendswood, TX) followed by a secondary purification on Qiagen RNAeasy Mini columns (Qiagen, Valencia, CA). RNA quality was assessed by Agilent bioanalyzer and RNA Integrity Numbers (RIN) for samples were >9.9."	"Total RNA (10 ug) was labeled by One-Cycle Target Labeling Kit as specified by Affymetrix."	"Hybridization, washing and staining were carried out according to the Affymetrix’s instructions."	"no additional information"	"Default normalization steps recommended by GeneSpring software were used:;	(1) data transformation: set measurements less than 0.01 to 0.01;	(2) per chip: normalize to 50th percentile;	(3) per gene: normalize to median"	"Name: DONG-SOON BAE;	Email: phmdxb@gwumc.edu;	Phone: 202-994-0964;	Fax: 202-994-2870;	Department: Pharmacology & Physiology;	Institute: George Washinton Uni.;	Address: 2300 I Street, NW;	City: Washington;	State: DC;	Zip/postal_code: 20037;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM307nnn/GSM307033/GSM307033.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM307nnn/GSM307033/GSM307033.CHP.gz"	54675	1	"download/GSM307033.CEL.gz"	"download/GSM307033.CEL"	5156525	13550577	64	1
279233	"HLF 1-3 (No)"	"GSM307052"	"GSE12205"	"GPL570"	"Public on Dec 02 2008"	"2008-07-22"	"2008-12-02"	"RNA"	"Human lung fibroblasts"	"Homo sapiens"	"Normal diploid human lung fibroblast cell line, LL24, was originally isolated from normal autopsy tissue of an 11-year-old male."	"total RNA"	"biotin"	"culture medium for 24hr"	"Following 24hr treatment with culture medium, RNA was isolated using RNA-Bee (Tel-Test, Friendswood, TX) followed by a secondary purification on Qiagen RNAeasy Mini columns (Qiagen, Valencia, CA). RNA quality was assessed by Agilent bioanalyzer and RNA Integrity Numbers (RIN) for samples were >9.9."	"Total RNA (10 ug) was labeled by One-Cycle Target Labeling Kit as specified by Affymetrix."	"Hybridization, washing and staining were carried out according to the Affymetrix’s instructions."	"no additional information"	"Default normalization steps recommended by GeneSpring software were used:;	(1) data transformation: set measurements less than 0.01 to 0.01;	(2) per chip: normalize to 50th percentile;	(3) per gene: normalize to median"	"Name: DONG-SOON BAE;	Email: phmdxb@gwumc.edu;	Phone: 202-994-0964;	Fax: 202-994-2870;	Department: Pharmacology & Physiology;	Institute: George Washinton Uni.;	Address: 2300 I Street, NW;	City: Washington;	State: DC;	Zip/postal_code: 20037;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM307nnn/GSM307052/GSM307052.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM307nnn/GSM307052/GSM307052.CHP.gz"	54675	1	"download/GSM307052.CEL.gz"	"download/GSM307052.CEL"	4662476	13551948	64	1
279235	"HLF 1-4 (No)"	"GSM307054"	"GSE12205"	"GPL570"	"Public on Dec 02 2008"	"2008-07-22"	"2008-12-02"	"RNA"	"Human lung fibroblasts"	"Homo sapiens"	"Normal diploid human lung fibroblast cell line, LL24, was originally isolated from normal autopsy tissue of an 11-year-old male."	"total RNA"	"biotin"	"culture medium for 24hr"	"Following 24hr treatment with culture medium, RNA was isolated using RNA-Bee (Tel-Test, Friendswood, TX) followed by a secondary purification on Qiagen RNAeasy Mini columns (Qiagen, Valencia, CA). RNA quality was assessed by Agilent bioanalyzer and RNA Integrity Numbers (RIN) for samples were >9.9."	"Total RNA (10 ug) was labeled by One-Cycle Target Labeling Kit as specified by Affymetrix."	"Hybridization, washing and staining were carried out according to the Affymetrix’s instructions."	"no additional information"	"Default normalization steps recommended by GeneSpring software were used:;	(1) data transformation: set measurements less than 0.01 to 0.01;	(2) per chip: normalize to 50th percentile;	(3) per gene: normalize to median"	"Name: DONG-SOON BAE;	Email: phmdxb@gwumc.edu;	Phone: 202-994-0964;	Fax: 202-994-2870;	Department: Pharmacology & Physiology;	Institute: George Washinton Uni.;	Address: 2300 I Street, NW;	City: Washington;	State: DC;	Zip/postal_code: 20037;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM307nnn/GSM307054/GSM307054.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM307nnn/GSM307054/GSM307054.CHP.gz"	54675	1	"download/GSM307054.CEL.gz"	"download/GSM307054.CEL"	4563692	13552821	64	1
279236	"HLF 3-1 (Cr)"	"GSM307059"	"GSE12205"	"GPL570"	"Public on Dec 02 2008"	"2008-07-22"	"2008-12-02"	"RNA"	"Human lung fibroblasts"	"Homo sapiens"	"Normal diploid human lung fibroblast cell line, LL24, was originally isolated from normal autopsy tissue of an 11-year-old male."	"total RNA"	"biotin"	"Sodium chromate [Cr(VI)] for 24hr"	"Following 24hr treatment with 1uM Cr(VI), RNA was isolated using RNA-Bee (Tel-Test, Friendswood, TX) followed by a secondary purification on Qiagen RNAeasy Mini columns (Qiagen, Valencia, CA). RNA quality was assessed by Agilent bioanalyzer and RNA Integrity Numbers (RIN) for samples were >9.9."	"Total RNA (10 ug) was labeled by One-Cycle Target Labeling Kit as specified by Affymetrix."	"Hybridization, washing and staining were carried out according to the Affymetrix’s instructions."	"no additional information"	"Default normalization steps recommended by GeneSpring software were used:;	(1) data transformation: set measurements less than 0.01 to 0.01;	(2) per chip: normalize to 50th percentile;	(3) per gene: normalize to median"	"Name: DONG-SOON BAE;	Email: phmdxb@gwumc.edu;	Phone: 202-994-0964;	Fax: 202-994-2870;	Department: Pharmacology & Physiology;	Institute: George Washinton Uni.;	Address: 2300 I Street, NW;	City: Washington;	State: DC;	Zip/postal_code: 20037;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM307nnn/GSM307059/GSM307059.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM307nnn/GSM307059/GSM307059.CHP.gz"	54675	1	"download/GSM307059.CEL.gz"	"download/GSM307059.CEL"	5089374	13551017	64	1
279237	"HLF 3-2 (Cr)"	"GSM307060"	"GSE12205"	"GPL570"	"Public on Dec 02 2008"	"2008-07-22"	"2008-12-02"	"RNA"	"Human lung fibroblasts"	"Homo sapiens"	"Normal diploid human lung fibroblast cell line, LL24, was originally isolated from normal autopsy tissue of an 11-year-old male."	"total RNA"	"biotin"	"Sodium chromate [Cr(VI)] for 24hr"	"Following 24hr treatment with 1uM Cr(VI), RNA was isolated using RNA-Bee (Tel-Test, Friendswood, TX) followed by a secondary purification on Qiagen RNAeasy Mini columns (Qiagen, Valencia, CA). RNA quality was assessed by Agilent bioanalyzer and RNA Integrity Numbers (RIN) for samples were >9.9."	"Total RNA (10 ug) was labeled by One-Cycle Target Labeling Kit as specified by Affymetrix."	"Hybridization, washing and staining were carried out according to the Affymetrix’s instructions."	"no additional information"	"Default normalization steps recommended by GeneSpring software were used:;	(1) data transformation: set measurements less than 0.01 to 0.01;	(2) per chip: normalize to 50th percentile;	(3) per gene: normalize to median"	"Name: DONG-SOON BAE;	Email: phmdxb@gwumc.edu;	Phone: 202-994-0964;	Fax: 202-994-2870;	Department: Pharmacology & Physiology;	Institute: George Washinton Uni.;	Address: 2300 I Street, NW;	City: Washington;	State: DC;	Zip/postal_code: 20037;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM307nnn/GSM307060/GSM307060.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM307nnn/GSM307060/GSM307060.CHP.gz"	54675	1	"download/GSM307060.CEL.gz"	"download/GSM307060.CEL"	5174177	13551441	64	1
279238	"HLF 3-3 (Cr)"	"GSM307061"	"GSE12205"	"GPL570"	"Public on Dec 02 2008"	"2008-07-22"	"2008-12-02"	"RNA"	"Human lung fibroblasts"	"Homo sapiens"	"Normal diploid human lung fibroblast cell line, LL24, was originally isolated from normal autopsy tissue of an 11-year-old male."	"total RNA"	"biotin"	"Sodium chromate [Cr(VI)] for 24hr"	"Following 24hr treatment with 1uM Cr(VI), RNA was isolated using RNA-Bee (Tel-Test, Friendswood, TX) followed by a secondary purification on Qiagen RNAeasy Mini columns (Qiagen, Valencia, CA). RNA quality was assessed by Agilent bioanalyzer and RNA Integrity Numbers (RIN) for samples were >9.9."	"Total RNA (10 ug) was labeled by One-Cycle Target Labeling Kit as specified by Affymetrix."	"Hybridization, washing and staining were carried out according to the Affymetrix’s instructions."	"no additional information"	"Default normalization steps recommended by GeneSpring software were used:;	(1) data transformation: set measurements less than 0.01 to 0.01;	(2) per chip: normalize to 50th percentile;	(3) per gene: normalize to median"	"Name: DONG-SOON BAE;	Email: phmdxb@gwumc.edu;	Phone: 202-994-0964;	Fax: 202-994-2870;	Department: Pharmacology & Physiology;	Institute: George Washinton Uni.;	Address: 2300 I Street, NW;	City: Washington;	State: DC;	Zip/postal_code: 20037;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM307nnn/GSM307061/GSM307061.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM307nnn/GSM307061/GSM307061.CHP.gz"	54675	1	"download/GSM307061.CEL.gz"	"download/GSM307061.CEL"	4629385	13553693	64	1
279239	"HLF 3-4 (Cr)"	"GSM307063"	"GSE12205"	"GPL570"	"Public on Dec 02 2008"	"2008-07-22"	"2008-12-02"	"RNA"	"Human lung fibroblasts"	"Homo sapiens"	"Normal diploid human lung fibroblast cell line, LL24, was originally isolated from normal autopsy tissue of an 11-year-old male."	"total RNA"	"biotin"	"Sodium chromate [Cr(VI)] for 24hr"	"Following 24hr treatment with 1uM Cr(VI), RNA was isolated using RNA-Bee (Tel-Test, Friendswood, TX) followed by a secondary purification on Qiagen RNAeasy Mini columns (Qiagen, Valencia, CA). RNA quality was assessed by Agilent bioanalyzer and RNA Integrity Numbers (RIN) for samples were >9.9."	"Total RNA (10 ug) was labeled by One-Cycle Target Labeling Kit as specified by Affymetrix."	"Hybridization, washing and staining were carried out according to the Affymetrix’s instructions."	"no additional information"	"Default normalization steps recommended by GeneSpring software were used:;	(1) data transformation: set measurements less than 0.01 to 0.01;	(2) per chip: normalize to 50th percentile;	(3) per gene: normalize to median"	"Name: DONG-SOON BAE;	Email: phmdxb@gwumc.edu;	Phone: 202-994-0964;	Fax: 202-994-2870;	Department: Pharmacology & Physiology;	Institute: George Washinton Uni.;	Address: 2300 I Street, NW;	City: Washington;	State: DC;	Zip/postal_code: 20037;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM307nnn/GSM307063/GSM307063.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM307nnn/GSM307063/GSM307063.CHP.gz"	54675	1	"download/GSM307063.CEL.gz"	"download/GSM307063.CEL"	4702133	13552196	64	1
279247	"HLF 4-1 (SOV+Cr)"	"GSM307073"	"GSE12205"	"GPL570"	"Public on Dec 02 2008"	"2008-07-22"	"2008-12-02"	"RNA"	"Human lung fibroblasts"	"Homo sapiens"	"Normal diploid human lung fibroblast cell line, LL24, was originally isolated from normal autopsy tissue of an 11-year-old male."	"total RNA"	"biotin"	"Sodium chromate [Cr(VI)] in the presence of SOV for 24hr"	"Following 24hr treatment with 1uM Cr(VI) + 10uM SOV, RNA was isolated using RNA-Bee (Tel-Test, Friendswood, TX) followed by a secondary purification on Qiagen RNAeasy Mini columns (Qiagen, Valencia, CA). RNA quality was assessed by Agilent bioanalyzer and RNA Integrity Numbers (RIN) for samples were >9.9."	"Total RNA (10 ug) was labeled by One-Cycle Target Labeling Kit as specified by Affymetrix."	"Hybridization, washing and staining were carried out according to the Affymetrix’s instructions."	"no additional information"	"Default normalization steps recommended by GeneSpring software were used:;	(1) data transformation: set measurements less than 0.01 to 0.01;	(2) per chip: normalize to 50th percentile;	(3) per gene: normalize to median"	"Name: DONG-SOON BAE;	Email: phmdxb@gwumc.edu;	Phone: 202-994-0964;	Fax: 202-994-2870;	Department: Pharmacology & Physiology;	Institute: George Washinton Uni.;	Address: 2300 I Street, NW;	City: Washington;	State: DC;	Zip/postal_code: 20037;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM307nnn/GSM307073/GSM307073.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM307nnn/GSM307073/GSM307073.CHP.gz"	54675	1	"download/GSM307073.CEL.gz"	"download/GSM307073.CEL"	5139850	13551585	64	1
279248	"HLF 4-2 (SOV+Cr)"	"GSM307074"	"GSE12205"	"GPL570"	"Public on Dec 02 2008"	"2008-07-22"	"2008-12-02"	"RNA"	"Human lung fibroblasts"	"Homo sapiens"	"Normal diploid human lung fibroblast cell line, LL24, was originally isolated from normal autopsy tissue of an 11-year-old male."	"total RNA"	"biotin"	"Sodium chromate [Cr(VI)] in the presence of SOV for 24hr"	"Following 24hr treatment with 1uM Cr(VI) + 10uM SOV, RNA was isolated using RNA-Bee (Tel-Test, Friendswood, TX) followed by a secondary purification on Qiagen RNAeasy Mini columns (Qiagen, Valencia, CA). RNA quality was assessed by Agilent bioanalyzer and RNA Integrity Numbers (RIN) for samples were >9.9."	"Total RNA (10 ug) was labeled by One-Cycle Target Labeling Kit as specified by Affymetrix."	"Hybridization, washing and staining were carried out according to the Affymetrix’s instructions."	"no additional information"	"Default normalization steps recommended by GeneSpring software were used:;	(1) data transformation: set measurements less than 0.01 to 0.01;	(2) per chip: normalize to 50th percentile;	(3) per gene: normalize to median"	"Name: DONG-SOON BAE;	Email: phmdxb@gwumc.edu;	Phone: 202-994-0964;	Fax: 202-994-2870;	Department: Pharmacology & Physiology;	Institute: George Washinton Uni.;	Address: 2300 I Street, NW;	City: Washington;	State: DC;	Zip/postal_code: 20037;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM307nnn/GSM307074/GSM307074.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM307nnn/GSM307074/GSM307074.CHP.gz"	54675	1	"download/GSM307074.CEL.gz"	"download/GSM307074.CEL"	5120839	13550588	64	1
279249	"HLF 4-3 (SOV+Cr)"	"GSM307075"	"GSE12205"	"GPL570"	"Public on Dec 02 2008"	"2008-07-22"	"2008-12-02"	"RNA"	"Human lung fibroblasts"	"Homo sapiens"	"Normal diploid human lung fibroblast cell line, LL24, was originally isolated from normal autopsy tissue of an 11-year-old male."	"total RNA"	"biotin"	"Sodium chromate [Cr(VI)] in the presence of SOV for 24hr"	"Following 24hr treatment with 1uM Cr(VI) + 10uM SOV, RNA was isolated using RNA-Bee (Tel-Test, Friendswood, TX) followed by a secondary purification on Qiagen RNAeasy Mini columns (Qiagen, Valencia, CA). RNA quality was assessed by Agilent bioanalyzer and RNA Integrity Numbers (RIN) for samples were >9.9."	"Total RNA (10 ug) was labeled by One-Cycle Target Labeling Kit as specified by Affymetrix."	"Hybridization, washing and staining were carried out according to the Affymetrix’s instructions."	"no additional information"	"Default normalization steps recommended by GeneSpring software were used:;	(1) data transformation: set measurements less than 0.01 to 0.01;	(2) per chip: normalize to 50th percentile;	(3) per gene: normalize to median"	"Name: DONG-SOON BAE;	Email: phmdxb@gwumc.edu;	Phone: 202-994-0964;	Fax: 202-994-2870;	Department: Pharmacology & Physiology;	Institute: George Washinton Uni.;	Address: 2300 I Street, NW;	City: Washington;	State: DC;	Zip/postal_code: 20037;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM307nnn/GSM307075/GSM307075.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM307nnn/GSM307075/GSM307075.CHP.gz"	54675	1	"download/GSM307075.CEL.gz"	"download/GSM307075.CEL"	4606247	13552492	64	1
279251	"HLF 4-4 (SOV+Cr)"	"GSM307077"	"GSE12205"	"GPL570"	"Public on Dec 02 2008"	"2008-07-22"	"2008-12-02"	"RNA"	"Human lung fibroblasts"	"Homo sapiens"	"Normal diploid human lung fibroblast cell line, LL24, was originally isolated from normal autopsy tissue of an 11-year-old male."	"total RNA"	"biotin"	"Sodium chromate [Cr(VI)] in the presence of SOV for 24hr"	"Following 24hr treatment with 1uM Cr(VI) + 10uM SOV, RNA was isolated using RNA-Bee (Tel-Test, Friendswood, TX) followed by a secondary purification on Qiagen RNAeasy Mini columns (Qiagen, Valencia, CA). RNA quality was assessed by Agilent bioanalyzer and RNA Integrity Numbers (RIN) for samples were >9.9."	"Total RNA (10 ug) was labeled by One-Cycle Target Labeling Kit as specified by Affymetrix."	"Hybridization, washing and staining were carried out according to the Affymetrix’s instructions."	"no additional information"	"Default normalization steps recommended by GeneSpring software were used:;	(1) data transformation: set measurements less than 0.01 to 0.01;	(2) per chip: normalize to 50th percentile;	(3) per gene: normalize to median"	"Name: DONG-SOON BAE;	Email: phmdxb@gwumc.edu;	Phone: 202-994-0964;	Fax: 202-994-2870;	Department: Pharmacology & Physiology;	Institute: George Washinton Uni.;	Address: 2300 I Street, NW;	City: Washington;	State: DC;	Zip/postal_code: 20037;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM307nnn/GSM307077/GSM307077.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM307nnn/GSM307077/GSM307077.CHP.gz"	54675	1	"download/GSM307077.CEL.gz"	"download/GSM307077.CEL"	4658182	13552345	64	1
289020	"22038"	"GSM318094"	"GSE12667"	"GPL570"	"Public on Sep 05 2008"	"2008-09-04"	"2008-11-18"	"RNA"	"Lung"	"Homo sapiens"	"Race: African American;	Gender: M;	TSP_Patient# 24255;	Smoking_Status: Current;	Pathology: Other"	"total RNA"	"biotin"	"No treatment. Disease state only"	"RNA extracted with Trizol"	"Chips labeled with biotin according to Manufacturer's protocol"	"Chips hybridized according to Manufacturer's protocol"	"11705"	"Data corrected to 1500 Baseline"	"Name: Rekha Meyer;	Email: rmeyer@pathbox.wustl.edu;	Institute: Washington University School of Medicine;	Address: 4320 Forest Park Av;	City: St Louis;	State: MO;	Zip/postal_code: 63128;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM318nnn/GSM318094/GSM318094.CEL.gz"	54675	1	"download/GSM318094.CEL.gz"	"download/GSM318094.CEL"	4566677	13551191	64	1
289055	"22090"	"GSM318129"	"GSE12667"	"GPL570"	"Public on Sep 05 2008"	"2008-09-04"	"2008-11-18"	"RNA"	"Lung"	"Homo sapiens"	"Race: White;	Gender: M;	TSP_Patient# 24323;	Smoking_Status: Not Available;	Pathology: Other"	"total RNA"	"biotin"	"No treatment. Disease state only"	"RNA extracted with Trizol"	"Chips labeled with biotin according to Manufacturer's protocol"	"Chips hybridized according to Manufacturer's protocol"	"11784"	"Data corrected to 1500 Baseline"	"Name: Rekha Meyer;	Email: rmeyer@pathbox.wustl.edu;	Institute: Washington University School of Medicine;	Address: 4320 Forest Park Av;	City: St Louis;	State: MO;	Zip/postal_code: 63128;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM318nnn/GSM318129/GSM318129.CEL.gz"	54675	1	"download/GSM318129.CEL.gz"	"download/GSM318129.CEL"	4506248	13552742	64	1
400930	"Lung siTUG1 Replicate1"	"GSM452271"	"GSE16226"	"GPL570"	"Public on Sep 14 2009"	"2009-09-14"	"2009-09-14"	"RNA"	"Primary Lung Fibroblasts, siRNA-transfected"	"Homo sapiens"	"tissue: lung;	cell type: primary fibroblasts;	sirna: siTUG1;	replicate: 1"	"total RNA"	"Biotin"	NA	"Trizol"	"Standard Affymetrix protocols for Human U133 Plus 2.0 Array"	"Standard Affymetrix protocols for Human U133 Plus 2.0 Array"	"lincRNA knock downs"	"RMA"	"Name: Mitchell Guttman;	Email: mguttman@mit.edu;	Institute: Broad Institute;	Address: 7 Cambridge Center;	City: Cambridge;	State: MA;	Zip/postal_code: 02139;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM452nnn/GSM452271/GSM452271.CEL.gz"	54675	1	"download/GSM452271.CEL.gz"	"download/GSM452271.CEL"	4988057	13550530	64	1
400931	"Lung siTUG1 Replicate2"	"GSM452272"	"GSE16226"	"GPL570"	"Public on Sep 14 2009"	"2009-09-14"	"2009-09-14"	"RNA"	"Primary Lung Fibroblasts, siRNA-transfected"	"Homo sapiens"	"tissue: lung;	cell type: primary fibroblasts;	sirna: siTUG1;	replicate: 2"	"total RNA"	"Biotin"	NA	"Trizol"	"Standard Affymetrix protocols for Human U133 Plus 2.0 Array"	"Standard Affymetrix protocols for Human U133 Plus 2.0 Array"	"lincRNA knock downs"	"RMA"	"Name: Mitchell Guttman;	Email: mguttman@mit.edu;	Institute: Broad Institute;	Address: 7 Cambridge Center;	City: Cambridge;	State: MA;	Zip/postal_code: 02139;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM452nnn/GSM452272/GSM452272.CEL.gz"	54675	1	"download/GSM452272.CEL.gz"	"download/GSM452272.CEL"	5087545	13550379	64	1
400932	"Lung siTUG1 Replicate3"	"GSM452273"	"GSE16226"	"GPL570"	"Public on Sep 14 2009"	"2009-09-14"	"2009-09-14"	"RNA"	"Primary Lung Fibroblasts, siRNA-transfected"	"Homo sapiens"	"tissue: lung;	cell type: primary fibroblasts;	sirna: siTUG1;	replicate: 3"	"total RNA"	"Biotin"	NA	"Trizol"	"Standard Affymetrix protocols for Human U133 Plus 2.0 Array"	"Standard Affymetrix protocols for Human U133 Plus 2.0 Array"	"lincRNA knock downs"	"RMA"	"Name: Mitchell Guttman;	Email: mguttman@mit.edu;	Institute: Broad Institute;	Address: 7 Cambridge Center;	City: Cambridge;	State: MA;	Zip/postal_code: 02139;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM452nnn/GSM452273/GSM452273.CEL.gz"	54675	1	"download/GSM452273.CEL.gz"	"download/GSM452273.CEL"	4869611	13550386	64	1
400933	"Lung siScramble Replicate1"	"GSM452274"	"GSE16226"	"GPL570"	"Public on Sep 14 2009"	"2009-09-14"	"2009-09-14"	"RNA"	"Primary Lung Fibroblasts, siRNA-transfected"	"Homo sapiens"	"tissue: lung;	cell type: primary fibroblasts;	sirna: Non-targetting siRNA Control;	replicate: 1"	"total RNA"	"Biotin"	NA	"Trizol"	"Standard Affymetrix protocols for Human U133 Plus 2.0 Array"	"Standard Affymetrix protocols for Human U133 Plus 2.0 Array"	"lincRNA knock downs"	"RMA"	"Name: Mitchell Guttman;	Email: mguttman@mit.edu;	Institute: Broad Institute;	Address: 7 Cambridge Center;	City: Cambridge;	State: MA;	Zip/postal_code: 02139;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM452nnn/GSM452274/GSM452274.CEL.gz"	54675	1	"download/GSM452274.CEL.gz"	"download/GSM452274.CEL"	4949260	13550239	64	1
400934	"Lung siScramble Replicate2"	"GSM452275"	"GSE16226"	"GPL570"	"Public on Sep 14 2009"	"2009-09-14"	"2009-09-14"	"RNA"	"Primary Lung Fibroblasts, siRNA-transfected"	"Homo sapiens"	"tissue: lung;	cell type: primary fibroblasts;	sirna: Non-targetting siRNA Control;	replicate: 2"	"total RNA"	"Biotin"	NA	"Trizol"	"Standard Affymetrix protocols for Human U133 Plus 2.0 Array"	"Standard Affymetrix protocols for Human U133 Plus 2.0 Array"	"lincRNA knock downs"	"RMA"	"Name: Mitchell Guttman;	Email: mguttman@mit.edu;	Institute: Broad Institute;	Address: 7 Cambridge Center;	City: Cambridge;	State: MA;	Zip/postal_code: 02139;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM452nnn/GSM452275/GSM452275.CEL.gz"	54675	1	"download/GSM452275.CEL.gz"	"download/GSM452275.CEL"	5095595	13550351	64	1
400935	"Lung siScramble Replicate3"	"GSM452276"	"GSE16226"	"GPL570"	"Public on Sep 14 2009"	"2009-09-14"	"2009-09-14"	"RNA"	"Primary Lung Fibroblasts, siRNA-transfected"	"Homo sapiens"	"tissue: lung;	cell type: primary fibroblasts;	sirna: Non-targetting siRNA Control;	replicate: 3"	"total RNA"	"Biotin"	NA	"Trizol"	"Standard Affymetrix protocols for Human U133 Plus 2.0 Array"	"Standard Affymetrix protocols for Human U133 Plus 2.0 Array"	"lincRNA knock downs"	"RMA"	"Name: Mitchell Guttman;	Email: mguttman@mit.edu;	Institute: Broad Institute;	Address: 7 Cambridge Center;	City: Cambridge;	State: MA;	Zip/postal_code: 02139;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM452nnn/GSM452276/GSM452276.CEL.gz"	54675	1	"download/GSM452276.CEL.gz"	"download/GSM452276.CEL"	5131172	13550290	64	1
407185	"normal human bronchial epithelial cell line treated with 5-AZA rep 1"	"GSM459743"	"GSE18454"	"GPL570"	"Public on Oct 07 2010"	"2009-10-07"	"2009-10-07"	"RNA"	"NHBE AZA rep 1"	"Homo sapiens"	"tissue: Lung;	cell line: NHBE;	agent: 5-aza-dC and TSA"	"total RNA"	"Biotin"	"NHBE and SAEC cells were split to low density (1×106 cells/T-75 flask) 24 hours before treatment. Stock solutions of 5Aza-dC (Sigma, St. Louis, MO) and TSA (Sigma) were dissolved in 50% Acetic Acid or 100% ethanol, respectively. Cells were treated with 5 µM 5-Aza-deoxycytidine for 3 days and 300 nM TSA for last 24 hours. Baseline expression was established by mock-treated cells with the same volume of 50% Acetic Acid or ethanol."	"Total cellular RNA was isolated using Trizol (Life Technologies, Gaithersburg, MD) and the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions."	"T7 oligo(dT) primer (Sigma-Proligo) and 5ug total RNA are combined for first strand cDNA synthesis.  Following second strand cDNA synthesis and cDNA cleanup (Phase Lock Gel Light, Eppendorf , Hamburg, Germany) an in vitro transcription reaction is performed overnight using T7 RNA transcript labeling kit provided by Enzo Life Sciences, Inc. (Farmingdale, NY).  IVT reactions are cleaned up using RNeasy Mini Kit (Qiagen) and concentration determined via Nanodrop Spectrophotometer.  15ug cRNA is fragmented using 5X fragmentation buffer (made in-house)."	"Hybridization cocktail is made in accordance with Affymetrix eukaryotic expression array protocol (Affymetrix, Santa Clara, CA) and combined with fragmented cRNA.  10ug cRNA is loaded onto Human U133Plus 2.0 genome arrays (Affymetrix, Santa Clara, CA) and hybridized overnight for 16 hours.  After hybridization, staining and washing of the arrays was performed following the Affymetrix eukaryotic expression array protocol, including staining with streptavidin-phycoerythrin, antibody stain, and a second streptavidin-phycoerythrin stain."	"no additional information"	"Raw analysis performed with Affymetrix GeneChip Operating System (GCOS) 1.4"	"Name: Chad Glazer;	Institute: Johns Hopkins Medical Institutions;	Address: 1550 Orleans St. CRB II-574;	City: Baltimore;	State: MD;	Zip/postal_code: 21231;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM459nnn/GSM459743/GSM459743.CEL.gz"	54613	1	"download/GSM459743.CEL.gz"	"download/GSM459743.CEL"	5191965	13550811	64	1
407186	"normal human bronchial epithelial cell line treated with 5-AZA rep 2"	"GSM459744"	"GSE18454"	"GPL570"	"Public on Oct 07 2010"	"2009-10-07"	"2009-10-07"	"RNA"	"NHBE AZA rep 2"	"Homo sapiens"	"tissue: Lung;	cell line: NHBE;	agent: 5-aza-dC and TSA"	"total RNA"	"Biotin"	"NHBE and SAEC cells were split to low density (1×106 cells/T-75 flask) 24 hours before treatment. Stock solutions of 5Aza-dC (Sigma, St. Louis, MO) and TSA (Sigma) were dissolved in 50% Acetic Acid or 100% ethanol, respectively. Cells were treated with 5 µM 5-Aza-deoxycytidine for 3 days and 300 nM TSA for last 24 hours. Baseline expression was established by mock-treated cells with the same volume of 50% Acetic Acid or ethanol."	"Total cellular RNA was isolated using Trizol (Life Technologies, Gaithersburg, MD) and the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions."	"T7 oligo(dT) primer (Sigma-Proligo) and 5ug total RNA are combined for first strand cDNA synthesis.  Following second strand cDNA synthesis and cDNA cleanup (Phase Lock Gel Light, Eppendorf , Hamburg, Germany) an in vitro transcription reaction is performed overnight using T7 RNA transcript labeling kit provided by Enzo Life Sciences, Inc. (Farmingdale, NY).  IVT reactions are cleaned up using RNeasy Mini Kit (Qiagen) and concentration determined via Nanodrop Spectrophotometer.  15ug cRNA is fragmented using 5X fragmentation buffer (made in-house)."	"Hybridization cocktail is made in accordance with Affymetrix eukaryotic expression array protocol (Affymetrix, Santa Clara, CA) and combined with fragmented cRNA.  10ug cRNA is loaded onto Human U133Plus 2.0 genome arrays (Affymetrix, Santa Clara, CA) and hybridized overnight for 16 hours.  After hybridization, staining and washing of the arrays was performed following the Affymetrix eukaryotic expression array protocol, including staining with streptavidin-phycoerythrin, antibody stain, and a second streptavidin-phycoerythrin stain."	"no additional information"	"Raw analysis performed with Affymetrix GeneChip Operating System (GCOS) 1.4"	"Name: Chad Glazer;	Institute: Johns Hopkins Medical Institutions;	Address: 1550 Orleans St. CRB II-574;	City: Baltimore;	State: MD;	Zip/postal_code: 21231;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM459nnn/GSM459744/GSM459744.CEL.gz"	54613	1	"download/GSM459744.CEL.gz"	"download/GSM459744.CEL"	5379124	13550683	64	1
407187	"normal human bronchial epithelial cell line treated with 5-AZA rep 3"	"GSM459745"	"GSE18454"	"GPL570"	"Public on Oct 07 2010"	"2009-10-07"	"2009-10-07"	"RNA"	"NHBE AZA rep 3"	"Homo sapiens"	"tissue: Lung;	cell line: NHBE;	agent: 5-aza-dC and TSA"	"total RNA"	"Biotin"	"NHBE and SAEC cells were split to low density (1×106 cells/T-75 flask) 24 hours before treatment. Stock solutions of 5Aza-dC (Sigma, St. Louis, MO) and TSA (Sigma) were dissolved in 50% Acetic Acid or 100% ethanol, respectively. Cells were treated with 5 µM 5-Aza-deoxycytidine for 3 days and 300 nM TSA for last 24 hours. Baseline expression was established by mock-treated cells with the same volume of 50% Acetic Acid or ethanol."	"Total cellular RNA was isolated using Trizol (Life Technologies, Gaithersburg, MD) and the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions."	"T7 oligo(dT) primer (Sigma-Proligo) and 5ug total RNA are combined for first strand cDNA synthesis.  Following second strand cDNA synthesis and cDNA cleanup (Phase Lock Gel Light, Eppendorf , Hamburg, Germany) an in vitro transcription reaction is performed overnight using T7 RNA transcript labeling kit provided by Enzo Life Sciences, Inc. (Farmingdale, NY).  IVT reactions are cleaned up using RNeasy Mini Kit (Qiagen) and concentration determined via Nanodrop Spectrophotometer.  15ug cRNA is fragmented using 5X fragmentation buffer (made in-house)."	"Hybridization cocktail is made in accordance with Affymetrix eukaryotic expression array protocol (Affymetrix, Santa Clara, CA) and combined with fragmented cRNA.  10ug cRNA is loaded onto Human U133Plus 2.0 genome arrays (Affymetrix, Santa Clara, CA) and hybridized overnight for 16 hours.  After hybridization, staining and washing of the arrays was performed following the Affymetrix eukaryotic expression array protocol, including staining with streptavidin-phycoerythrin, antibody stain, and a second streptavidin-phycoerythrin stain."	"no additional information"	"Raw analysis performed with Affymetrix GeneChip Operating System (GCOS) 1.4"	"Name: Chad Glazer;	Institute: Johns Hopkins Medical Institutions;	Address: 1550 Orleans St. CRB II-574;	City: Baltimore;	State: MD;	Zip/postal_code: 21231;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM459nnn/GSM459745/GSM459745.CEL.gz"	54613	1	"download/GSM459745.CEL.gz"	"download/GSM459745.CEL"	5288665	13550739	64	1
407188	"normal human bronchial epithelial cell line control rep 1"	"GSM459746"	"GSE18454"	"GPL570"	"Public on Oct 07 2010"	"2009-10-07"	"2009-10-07"	"RNA"	"NHBE control rep 1"	"Homo sapiens"	"tissue: Lung;	cell line: NHBE;	agent: mock-treated"	"total RNA"	"Biotin"	"NHBE and SAEC cells were split to low density (1×106 cells/T-75 flask) 24 hours before treatment. Stock solutions of 5Aza-dC (Sigma, St. Louis, MO) and TSA (Sigma) were dissolved in 50% Acetic Acid or 100% ethanol, respectively. Cells were treated with 5 µM 5-Aza-deoxycytidine for 3 days and 300 nM TSA for last 24 hours. Baseline expression was established by mock-treated cells with the same volume of 50% Acetic Acid or ethanol."	"Total cellular RNA was isolated using Trizol (Life Technologies, Gaithersburg, MD) and the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions."	"T7 oligo(dT) primer (Sigma-Proligo) and 5ug total RNA are combined for first strand cDNA synthesis.  Following second strand cDNA synthesis and cDNA cleanup (Phase Lock Gel Light, Eppendorf , Hamburg, Germany) an in vitro transcription reaction is performed overnight using T7 RNA transcript labeling kit provided by Enzo Life Sciences, Inc. (Farmingdale, NY).  IVT reactions are cleaned up using RNeasy Mini Kit (Qiagen) and concentration determined via Nanodrop Spectrophotometer.  15ug cRNA is fragmented using 5X fragmentation buffer (made in-house)."	"Hybridization cocktail is made in accordance with Affymetrix eukaryotic expression array protocol (Affymetrix, Santa Clara, CA) and combined with fragmented cRNA.  10ug cRNA is loaded onto Human U133Plus 2.0 genome arrays (Affymetrix, Santa Clara, CA) and hybridized overnight for 16 hours.  After hybridization, staining and washing of the arrays was performed following the Affymetrix eukaryotic expression array protocol, including staining with streptavidin-phycoerythrin, antibody stain, and a second streptavidin-phycoerythrin stain."	"no additional information"	"Raw analysis performed with Affymetrix GeneChip Operating System (GCOS) 1.4"	"Name: Chad Glazer;	Institute: Johns Hopkins Medical Institutions;	Address: 1550 Orleans St. CRB II-574;	City: Baltimore;	State: MD;	Zip/postal_code: 21231;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM459nnn/GSM459746/GSM459746.CEL.gz"	54613	1	"download/GSM459746.CEL.gz"	"download/GSM459746.CEL"	5351272	13551257	64	1
407189	"normal human bronchial epithelial cell line control rep 2"	"GSM459747"	"GSE18454"	"GPL570"	"Public on Oct 07 2010"	"2009-10-07"	"2009-10-07"	"RNA"	"NHBE control rep 2"	"Homo sapiens"	"tissue: Lung;	cell line: NHBE;	agent: mock-treated"	"total RNA"	"Biotin"	"NHBE and SAEC cells were split to low density (1×106 cells/T-75 flask) 24 hours before treatment. Stock solutions of 5Aza-dC (Sigma, St. Louis, MO) and TSA (Sigma) were dissolved in 50% Acetic Acid or 100% ethanol, respectively. Cells were treated with 5 µM 5-Aza-deoxycytidine for 3 days and 300 nM TSA for last 24 hours. Baseline expression was established by mock-treated cells with the same volume of 50% Acetic Acid or ethanol."	"Total cellular RNA was isolated using Trizol (Life Technologies, Gaithersburg, MD) and the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions."	"T7 oligo(dT) primer (Sigma-Proligo) and 5ug total RNA are combined for first strand cDNA synthesis.  Following second strand cDNA synthesis and cDNA cleanup (Phase Lock Gel Light, Eppendorf , Hamburg, Germany) an in vitro transcription reaction is performed overnight using T7 RNA transcript labeling kit provided by Enzo Life Sciences, Inc. (Farmingdale, NY).  IVT reactions are cleaned up using RNeasy Mini Kit (Qiagen) and concentration determined via Nanodrop Spectrophotometer.  15ug cRNA is fragmented using 5X fragmentation buffer (made in-house)."	"Hybridization cocktail is made in accordance with Affymetrix eukaryotic expression array protocol (Affymetrix, Santa Clara, CA) and combined with fragmented cRNA.  10ug cRNA is loaded onto Human U133Plus 2.0 genome arrays (Affymetrix, Santa Clara, CA) and hybridized overnight for 16 hours.  After hybridization, staining and washing of the arrays was performed following the Affymetrix eukaryotic expression array protocol, including staining with streptavidin-phycoerythrin, antibody stain, and a second streptavidin-phycoerythrin stain."	"no additional information"	"Raw analysis performed with Affymetrix GeneChip Operating System (GCOS) 1.4"	"Name: Chad Glazer;	Institute: Johns Hopkins Medical Institutions;	Address: 1550 Orleans St. CRB II-574;	City: Baltimore;	State: MD;	Zip/postal_code: 21231;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM459nnn/GSM459747/GSM459747.CEL.gz"	54613	1	"download/GSM459747.CEL.gz"	"download/GSM459747.CEL"	5318033	13550661	64	1
407190	"normal human bronchial epithelial cell line control rep 3"	"GSM459748"	"GSE18454"	"GPL570"	"Public on Oct 07 2010"	"2009-10-07"	"2009-10-07"	"RNA"	"NHBE control rep 3"	"Homo sapiens"	"tissue: Lung;	cell line: NHBE;	agent: mock-treated"	"total RNA"	"Biotin"	"NHBE and SAEC cells were split to low density (1×106 cells/T-75 flask) 24 hours before treatment. Stock solutions of 5Aza-dC (Sigma, St. Louis, MO) and TSA (Sigma) were dissolved in 50% Acetic Acid or 100% ethanol, respectively. Cells were treated with 5 µM 5-Aza-deoxycytidine for 3 days and 300 nM TSA for last 24 hours. Baseline expression was established by mock-treated cells with the same volume of 50% Acetic Acid or ethanol."	"Total cellular RNA was isolated using Trizol (Life Technologies, Gaithersburg, MD) and the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions."	"T7 oligo(dT) primer (Sigma-Proligo) and 5ug total RNA are combined for first strand cDNA synthesis.  Following second strand cDNA synthesis and cDNA cleanup (Phase Lock Gel Light, Eppendorf , Hamburg, Germany) an in vitro transcription reaction is performed overnight using T7 RNA transcript labeling kit provided by Enzo Life Sciences, Inc. (Farmingdale, NY).  IVT reactions are cleaned up using RNeasy Mini Kit (Qiagen) and concentration determined via Nanodrop Spectrophotometer.  15ug cRNA is fragmented using 5X fragmentation buffer (made in-house)."	"Hybridization cocktail is made in accordance with Affymetrix eukaryotic expression array protocol (Affymetrix, Santa Clara, CA) and combined with fragmented cRNA.  10ug cRNA is loaded onto Human U133Plus 2.0 genome arrays (Affymetrix, Santa Clara, CA) and hybridized overnight for 16 hours.  After hybridization, staining and washing of the arrays was performed following the Affymetrix eukaryotic expression array protocol, including staining with streptavidin-phycoerythrin, antibody stain, and a second streptavidin-phycoerythrin stain."	"no additional information"	"Raw analysis performed with Affymetrix GeneChip Operating System (GCOS) 1.4"	"Name: Chad Glazer;	Institute: Johns Hopkins Medical Institutions;	Address: 1550 Orleans St. CRB II-574;	City: Baltimore;	State: MD;	Zip/postal_code: 21231;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM459nnn/GSM459748/GSM459748.CEL.gz"	54613	1	"download/GSM459748.CEL.gz"	"download/GSM459748.CEL"	5347189	13550481	64	1
407191	"normal human small airway epithelial cell line treated with 5-AZA rep 1"	"GSM459749"	"GSE18454"	"GPL570"	"Public on Oct 07 2010"	"2009-10-07"	"2009-10-07"	"RNA"	"SAEC AZA rep 1"	"Homo sapiens"	"tissue: Lung;	cell line: SAEC;	agent: 5-aza-dC and TSA"	"total RNA"	"Biotin"	"NHBE and SAEC cells were split to low density (1×106 cells/T-75 flask) 24 hours before treatment. Stock solutions of 5Aza-dC (Sigma, St. Louis, MO) and TSA (Sigma) were dissolved in 50% Acetic Acid or 100% ethanol, respectively. Cells were treated with 5 µM 5-Aza-deoxycytidine for 3 days and 300 nM TSA for last 24 hours. Baseline expression was established by mock-treated cells with the same volume of 50% Acetic Acid or ethanol."	"Total cellular RNA was isolated using Trizol (Life Technologies, Gaithersburg, MD) and the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions."	"T7 oligo(dT) primer (Sigma-Proligo) and 5ug total RNA are combined for first strand cDNA synthesis.  Following second strand cDNA synthesis and cDNA cleanup (Phase Lock Gel Light, Eppendorf , Hamburg, Germany) an in vitro transcription reaction is performed overnight using T7 RNA transcript labeling kit provided by Enzo Life Sciences, Inc. (Farmingdale, NY).  IVT reactions are cleaned up using RNeasy Mini Kit (Qiagen) and concentration determined via Nanodrop Spectrophotometer.  15ug cRNA is fragmented using 5X fragmentation buffer (made in-house)."	"Hybridization cocktail is made in accordance with Affymetrix eukaryotic expression array protocol (Affymetrix, Santa Clara, CA) and combined with fragmented cRNA.  10ug cRNA is loaded onto Human U133Plus 2.0 genome arrays (Affymetrix, Santa Clara, CA) and hybridized overnight for 16 hours.  After hybridization, staining and washing of the arrays was performed following the Affymetrix eukaryotic expression array protocol, including staining with streptavidin-phycoerythrin, antibody stain, and a second streptavidin-phycoerythrin stain."	"no additional information"	"Raw analysis performed with Affymetrix GeneChip Operating System (GCOS) 1.4"	"Name: Chad Glazer;	Institute: Johns Hopkins Medical Institutions;	Address: 1550 Orleans St. CRB II-574;	City: Baltimore;	State: MD;	Zip/postal_code: 21231;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM459nnn/GSM459749/GSM459749.CEL.gz"	54613	1	"download/GSM459749.CEL.gz"	"download/GSM459749.CEL"	5157523	13550807	64	1
407192	"normal human small airway epithelial cell line treated with 5-AZA rep 2"	"GSM459750"	"GSE18454"	"GPL570"	"Public on Oct 07 2010"	"2009-10-07"	"2009-10-07"	"RNA"	"SAEC AZA rep 2"	"Homo sapiens"	"tissue: Lung;	cell line: SAEC;	agent: 5-aza-dC and TSA"	"total RNA"	"Biotin"	"NHBE and SAEC cells were split to low density (1×106 cells/T-75 flask) 24 hours before treatment. Stock solutions of 5Aza-dC (Sigma, St. Louis, MO) and TSA (Sigma) were dissolved in 50% Acetic Acid or 100% ethanol, respectively. Cells were treated with 5 µM 5-Aza-deoxycytidine for 3 days and 300 nM TSA for last 24 hours. Baseline expression was established by mock-treated cells with the same volume of 50% Acetic Acid or ethanol."	"Total cellular RNA was isolated using Trizol (Life Technologies, Gaithersburg, MD) and the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions."	"T7 oligo(dT) primer (Sigma-Proligo) and 5ug total RNA are combined for first strand cDNA synthesis.  Following second strand cDNA synthesis and cDNA cleanup (Phase Lock Gel Light, Eppendorf , Hamburg, Germany) an in vitro transcription reaction is performed overnight using T7 RNA transcript labeling kit provided by Enzo Life Sciences, Inc. (Farmingdale, NY).  IVT reactions are cleaned up using RNeasy Mini Kit (Qiagen) and concentration determined via Nanodrop Spectrophotometer.  15ug cRNA is fragmented using 5X fragmentation buffer (made in-house)."	"Hybridization cocktail is made in accordance with Affymetrix eukaryotic expression array protocol (Affymetrix, Santa Clara, CA) and combined with fragmented cRNA.  10ug cRNA is loaded onto Human U133Plus 2.0 genome arrays (Affymetrix, Santa Clara, CA) and hybridized overnight for 16 hours.  After hybridization, staining and washing of the arrays was performed following the Affymetrix eukaryotic expression array protocol, including staining with streptavidin-phycoerythrin, antibody stain, and a second streptavidin-phycoerythrin stain."	"no additional information"	"Raw analysis performed with Affymetrix GeneChip Operating System (GCOS) 1.4"	"Name: Chad Glazer;	Institute: Johns Hopkins Medical Institutions;	Address: 1550 Orleans St. CRB II-574;	City: Baltimore;	State: MD;	Zip/postal_code: 21231;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM459nnn/GSM459750/GSM459750.CEL.gz"	54613	1	"download/GSM459750.CEL.gz"	"download/GSM459750.CEL"	5421168	13550663	64	1
407193	"normal human small airway epithelial cell line treated with 5-AZA rep 3"	"GSM459751"	"GSE18454"	"GPL570"	"Public on Oct 07 2010"	"2009-10-07"	"2009-10-07"	"RNA"	"SAEC AZA rep 3"	"Homo sapiens"	"tissue: Lung;	cell line: SAEC;	agent: 5-aza-dC and TSA"	"total RNA"	"Biotin"	"NHBE and SAEC cells were split to low density (1×106 cells/T-75 flask) 24 hours before treatment. Stock solutions of 5Aza-dC (Sigma, St. Louis, MO) and TSA (Sigma) were dissolved in 50% Acetic Acid or 100% ethanol, respectively. Cells were treated with 5 µM 5-Aza-deoxycytidine for 3 days and 300 nM TSA for last 24 hours. Baseline expression was established by mock-treated cells with the same volume of 50% Acetic Acid or ethanol."	"Total cellular RNA was isolated using Trizol (Life Technologies, Gaithersburg, MD) and the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions."	"T7 oligo(dT) primer (Sigma-Proligo) and 5ug total RNA are combined for first strand cDNA synthesis.  Following second strand cDNA synthesis and cDNA cleanup (Phase Lock Gel Light, Eppendorf , Hamburg, Germany) an in vitro transcription reaction is performed overnight using T7 RNA transcript labeling kit provided by Enzo Life Sciences, Inc. (Farmingdale, NY).  IVT reactions are cleaned up using RNeasy Mini Kit (Qiagen) and concentration determined via Nanodrop Spectrophotometer.  15ug cRNA is fragmented using 5X fragmentation buffer (made in-house)."	"Hybridization cocktail is made in accordance with Affymetrix eukaryotic expression array protocol (Affymetrix, Santa Clara, CA) and combined with fragmented cRNA.  10ug cRNA is loaded onto Human U133Plus 2.0 genome arrays (Affymetrix, Santa Clara, CA) and hybridized overnight for 16 hours.  After hybridization, staining and washing of the arrays was performed following the Affymetrix eukaryotic expression array protocol, including staining with streptavidin-phycoerythrin, antibody stain, and a second streptavidin-phycoerythrin stain."	"no additional information"	"Raw analysis performed with Affymetrix GeneChip Operating System (GCOS) 1.4"	"Name: Chad Glazer;	Institute: Johns Hopkins Medical Institutions;	Address: 1550 Orleans St. CRB II-574;	City: Baltimore;	State: MD;	Zip/postal_code: 21231;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM459nnn/GSM459751/GSM459751.CEL.gz"	54613	1	"download/GSM459751.CEL.gz"	"download/GSM459751.CEL"	4955467	13551115	64	1
407194	"normal human small airway epithelial cell line control rep 1"	"GSM459752"	"GSE18454"	"GPL570"	"Public on Oct 07 2010"	"2009-10-07"	"2009-10-07"	"RNA"	"SAEC control rep 1"	"Homo sapiens"	"tissue: Lung;	cell line: SAEC;	agent: mock-treated"	"total RNA"	"Biotin"	"NHBE and SAEC cells were split to low density (1×106 cells/T-75 flask) 24 hours before treatment. Stock solutions of 5Aza-dC (Sigma, St. Louis, MO) and TSA (Sigma) were dissolved in 50% Acetic Acid or 100% ethanol, respectively. Cells were treated with 5 µM 5-Aza-deoxycytidine for 3 days and 300 nM TSA for last 24 hours. Baseline expression was established by mock-treated cells with the same volume of 50% Acetic Acid or ethanol."	"Total cellular RNA was isolated using Trizol (Life Technologies, Gaithersburg, MD) and the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions."	"T7 oligo(dT) primer (Sigma-Proligo) and 5ug total RNA are combined for first strand cDNA synthesis.  Following second strand cDNA synthesis and cDNA cleanup (Phase Lock Gel Light, Eppendorf , Hamburg, Germany) an in vitro transcription reaction is performed overnight using T7 RNA transcript labeling kit provided by Enzo Life Sciences, Inc. (Farmingdale, NY).  IVT reactions are cleaned up using RNeasy Mini Kit (Qiagen) and concentration determined via Nanodrop Spectrophotometer.  15ug cRNA is fragmented using 5X fragmentation buffer (made in-house)."	"Hybridization cocktail is made in accordance with Affymetrix eukaryotic expression array protocol (Affymetrix, Santa Clara, CA) and combined with fragmented cRNA.  10ug cRNA is loaded onto Human U133Plus 2.0 genome arrays (Affymetrix, Santa Clara, CA) and hybridized overnight for 16 hours.  After hybridization, staining and washing of the arrays was performed following the Affymetrix eukaryotic expression array protocol, including staining with streptavidin-phycoerythrin, antibody stain, and a second streptavidin-phycoerythrin stain."	"no additional information"	"Raw analysis performed with Affymetrix GeneChip Operating System (GCOS) 1.4"	"Name: Chad Glazer;	Institute: Johns Hopkins Medical Institutions;	Address: 1550 Orleans St. CRB II-574;	City: Baltimore;	State: MD;	Zip/postal_code: 21231;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM459nnn/GSM459752/GSM459752.CEL.gz"	54613	1	"download/GSM459752.CEL.gz"	"download/GSM459752.CEL"	5342635	13550533	64	1
407195	"normal human small airway epithelial cell line control rep 2"	"GSM459753"	"GSE18454"	"GPL570"	"Public on Oct 07 2010"	"2009-10-07"	"2009-10-07"	"RNA"	"SAEC control rep 2"	"Homo sapiens"	"tissue: Lung;	cell line: SAEC;	agent: mock-treated"	"total RNA"	"Biotin"	"NHBE and SAEC cells were split to low density (1×106 cells/T-75 flask) 24 hours before treatment. Stock solutions of 5Aza-dC (Sigma, St. Louis, MO) and TSA (Sigma) were dissolved in 50% Acetic Acid or 100% ethanol, respectively. Cells were treated with 5 µM 5-Aza-deoxycytidine for 3 days and 300 nM TSA for last 24 hours. Baseline expression was established by mock-treated cells with the same volume of 50% Acetic Acid or ethanol."	"Total cellular RNA was isolated using Trizol (Life Technologies, Gaithersburg, MD) and the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions."	"T7 oligo(dT) primer (Sigma-Proligo) and 5ug total RNA are combined for first strand cDNA synthesis.  Following second strand cDNA synthesis and cDNA cleanup (Phase Lock Gel Light, Eppendorf , Hamburg, Germany) an in vitro transcription reaction is performed overnight using T7 RNA transcript labeling kit provided by Enzo Life Sciences, Inc. (Farmingdale, NY).  IVT reactions are cleaned up using RNeasy Mini Kit (Qiagen) and concentration determined via Nanodrop Spectrophotometer.  15ug cRNA is fragmented using 5X fragmentation buffer (made in-house)."	"Hybridization cocktail is made in accordance with Affymetrix eukaryotic expression array protocol (Affymetrix, Santa Clara, CA) and combined with fragmented cRNA.  10ug cRNA is loaded onto Human U133Plus 2.0 genome arrays (Affymetrix, Santa Clara, CA) and hybridized overnight for 16 hours.  After hybridization, staining and washing of the arrays was performed following the Affymetrix eukaryotic expression array protocol, including staining with streptavidin-phycoerythrin, antibody stain, and a second streptavidin-phycoerythrin stain."	"no additional information"	"Raw analysis performed with Affymetrix GeneChip Operating System (GCOS) 1.4"	"Name: Chad Glazer;	Institute: Johns Hopkins Medical Institutions;	Address: 1550 Orleans St. CRB II-574;	City: Baltimore;	State: MD;	Zip/postal_code: 21231;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM459nnn/GSM459753/GSM459753.CEL.gz"	54613	1	"download/GSM459753.CEL.gz"	"download/GSM459753.CEL"	5428179	13550537	64	1
407196	"normal human small airway epithelial cell line control rep 3"	"GSM459754"	"GSE18454"	"GPL570"	"Public on Oct 07 2010"	"2009-10-07"	"2009-10-07"	"RNA"	"SAEC control rep 3"	"Homo sapiens"	"tissue: Lung;	cell line: SAEC;	agent: mock-treated"	"total RNA"	"Biotin"	"NHBE and SAEC cells were split to low density (1×106 cells/T-75 flask) 24 hours before treatment. Stock solutions of 5Aza-dC (Sigma, St. Louis, MO) and TSA (Sigma) were dissolved in 50% Acetic Acid or 100% ethanol, respectively. Cells were treated with 5 µM 5-Aza-deoxycytidine for 3 days and 300 nM TSA for last 24 hours. Baseline expression was established by mock-treated cells with the same volume of 50% Acetic Acid or ethanol."	"Total cellular RNA was isolated using Trizol (Life Technologies, Gaithersburg, MD) and the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions."	"T7 oligo(dT) primer (Sigma-Proligo) and 5ug total RNA are combined for first strand cDNA synthesis.  Following second strand cDNA synthesis and cDNA cleanup (Phase Lock Gel Light, Eppendorf , Hamburg, Germany) an in vitro transcription reaction is performed overnight using T7 RNA transcript labeling kit provided by Enzo Life Sciences, Inc. (Farmingdale, NY).  IVT reactions are cleaned up using RNeasy Mini Kit (Qiagen) and concentration determined via Nanodrop Spectrophotometer.  15ug cRNA is fragmented using 5X fragmentation buffer (made in-house)."	"Hybridization cocktail is made in accordance with Affymetrix eukaryotic expression array protocol (Affymetrix, Santa Clara, CA) and combined with fragmented cRNA.  10ug cRNA is loaded onto Human U133Plus 2.0 genome arrays (Affymetrix, Santa Clara, CA) and hybridized overnight for 16 hours.  After hybridization, staining and washing of the arrays was performed following the Affymetrix eukaryotic expression array protocol, including staining with streptavidin-phycoerythrin, antibody stain, and a second streptavidin-phycoerythrin stain."	"no additional information"	"Raw analysis performed with Affymetrix GeneChip Operating System (GCOS) 1.4"	"Name: Chad Glazer;	Institute: Johns Hopkins Medical Institutions;	Address: 1550 Orleans St. CRB II-574;	City: Baltimore;	State: MD;	Zip/postal_code: 21231;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM459nnn/GSM459754/GSM459754.CEL.gz"	54613	1	"download/GSM459754.CEL.gz"	"download/GSM459754.CEL"	5215958	13550689	64	1
486750	"Control sample"	"GSM585112"	"GSE23704"	"GPL570"	"Public on Sep 04 2010"	"2010-08-19"	"2010-09-03"	"RNA"	"BAL cells from patients with inflammatory lung diseases"	"Homo sapiens"	"tissue: Lung;	agent: untreated;	age: Adults"	"total RNA"	"biotin"	"BAL cells cultivated either in the presence of liposomal ATRA (5µM) or left untreated for 3 days."	"Total RNA was extraction by using TRI reagent according to the manufacturer's instructions."	"According to the standard Affymetrix protocol"	"According to the standard Affymetrix protocol"	"Gene expression data from untreated BAL cells."	"Data were normalized, and transcript-specific gene expression levels were calculated, using gcrma (Wu et al., J. Comput. Biol., 12, 882-93, 2005; Wu et al., Nat. Biotechnol. 22, 656-8,, 2004) or rma (Bolstad et al., Bioinformatics, 19, 185-93, 2003; Irizarry et al., Nucleic Acids Res., 31, e15, 2003) as implemented in R (R Development Core Team, R foundation for statistical computing, Vienna, 2007) and Bioconductor (Gentleman et al., Genome Biology, 5, R80, 2004). Differentially expressed genes were identified using the permutation-based method of Tusher et al. (Proc. Natl. Acad. Sci. USA, 98, 5116-21, 2001) (sam) as implemented in the \samr\ R package, using the median false discovery rate over 100 data permutations as a measure for statistical significance."	"Name: Srinivas Mamidi;	Email: srinivas.mamidi@immu.uni-heidelberg.de;	Phone: +496221568121;	Department: Clinical Cooperation Group Inflammatory Lung Diseases;	Institute: Helmholtz Center Munich;	Address: Robert Koch Allee 29;	City: Gauting, Munich;	State: Bayern;	Zip/postal_code: 82131;	Country: Germany"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM585nnn/GSM585112/GSM585112.CEL.gz"	54675	1	"download/GSM585112.CEL.gz"	"download/GSM585112.CEL"	5047075	13550934	64	1
486751	"Liposomal ATRA treated sample"	"GSM585113"	"GSE23704"	"GPL570"	"Public on Sep 04 2010"	"2010-08-19"	"2010-09-03"	"RNA"	"BAL cells from patients with inflammatory lung diseases"	"Homo sapiens"	"tissue: Lung;	agent: liposomal ATRA (5µM);	age: Adults"	"total RNA"	"biotin"	"BAL cells cultivated either in the presence of liposomal ATRA (5µM) or left untreated for 3 days."	"Total RNA was extraction by using TRI reagent according to the manufacturer's instructions."	"According to the standard Affymetrix protocol"	"According to the standard Affymetrix protocol"	"Gene expression data from LipATRA treated BAL cells."	"Data were normalized, and transcript-specific gene expression levels were calculated, using gcrma (Wu et al., J. Comput. Biol., 12, 882-93, 2005; Wu et al., Nat. Biotechnol. 22, 656-8,, 2004) or rma (Bolstad et al., Bioinformatics, 19, 185-93, 2003; Irizarry et al., Nucleic Acids Res., 31, e15, 2003) as implemented in R (R Development Core Team, R foundation for statistical computing, Vienna, 2007) and Bioconductor (Gentleman et al., Genome Biology, 5, R80, 2004). Differentially expressed genes were identified using the permutation-based method of Tusher et al. (Proc. Natl. Acad. Sci. USA, 98, 5116-21, 2001) (sam) as implemented in the \samr\ R package, using the median false discovery rate over 100 data permutations as a measure for statistical significance."	"Name: Srinivas Mamidi;	Email: srinivas.mamidi@immu.uni-heidelberg.de;	Phone: +496221568121;	Department: Clinical Cooperation Group Inflammatory Lung Diseases;	Institute: Helmholtz Center Munich;	Address: Robert Koch Allee 29;	City: Gauting, Munich;	State: Bayern;	Zip/postal_code: 82131;	Country: Germany"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM585nnn/GSM585113/GSM585113.CEL.gz"	54675	1	"download/GSM585113.CEL.gz"	"download/GSM585113.CEL"	4966535	13551146	64	1
517459	"FS087 cell line, control, biological rep1"	"GSM654536"	"GSE26594"	"GPL570"	"Public on Jan 13 2011"	"2011-01-12"	"2011-01-13"	"RNA"	"Human primary lung fibroblast from an IPF patient maintained in standard culture"	"Homo sapiens"	"treatment group: Unstimulated;	cell type: Human primary lung fibroblast"	"total RNA"	"biotin"	"Each cell line was divided into two groups and half of each was treated with TNF-α (10 ng/ml) and IFN-γ (50 U/ml) added directly to the growing media and both groups allowed to incubate for 36 hr at standard conditions."	"Trizol extraction of total RNA was performed according to the manufacturer's instructions."	"Approximately 5 micrograms of total RNA was processed to produce biotinylated cRNA targets using the older (ENZO) Affymetrix protocol"	"standard Affymetrix procedures"	"FS087_control"	"GCRMA"	"Name: Michael Edwards;	Email: michael.edwards@ucdenver.edu;	Phone: 303-724-6054;	Fax: 303-724-6042;	Department: Pulmonary;	Institute: UC Denver;	Address: 12700 East 19th Avenue, Box C272;	City: Aurora;	State: CO;	Zip/postal_code: 80045;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM654nnn/GSM654536/GSM654536.CEL.gz"	54675	1	"download/GSM654536.CEL.gz"	"download/GSM654536.CEL"	4804798	13551491	64	1
517460	"FS087 cell line, stimulated, biological rep1"	"GSM654537"	"GSE26594"	"GPL570"	"Public on Jan 13 2011"	"2011-01-12"	"2011-01-13"	"RNA"	"Human primary lung fibroblast from an IPF patient treated for 36 hr with TNF-α (10 ng/ml) and IFN-γ (50 U/ml)."	"Homo sapiens"	"treatment group: TNF-α and IFN-γ stimulated;	cell type: Human primary lung fibroblast"	"total RNA"	"biotin"	"Each cell line was divided into two groups and half of each was treated with TNF-α (10 ng/ml) and IFN-γ (50 U/ml) added directly to the growing media and both groups allowed to incubate for 36 hr at standard conditions."	"Trizol extraction of total RNA was performed according to the manufacturer's instructions."	"Approximately 5 micrograms of total RNA was processed to produce biotinylated cRNA targets using the older (ENZO) Affymetrix protocol"	"standard Affymetrix procedures"	"FS087_stimulated"	"GCRMA"	"Name: Michael Edwards;	Email: michael.edwards@ucdenver.edu;	Phone: 303-724-6054;	Fax: 303-724-6042;	Department: Pulmonary;	Institute: UC Denver;	Address: 12700 East 19th Avenue, Box C272;	City: Aurora;	State: CO;	Zip/postal_code: 80045;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM654nnn/GSM654537/GSM654537.CEL.gz"	54675	1	"download/GSM654537.CEL.gz"	"download/GSM654537.CEL"	4827430	13550995	64	1
517463	"N78 cell line, control, biological rep3"	"GSM654540"	"GSE26594"	"GPL570"	"Public on Jan 13 2011"	"2011-01-12"	"2011-01-13"	"RNA"	"Human primary lung fibroblast from a control subject maintained in standard culture"	"Homo sapiens"	"treatment group: Unstimulated;	cell type: Human primary lung fibroblast"	"total RNA"	"biotin"	"Each cell line was divided into two groups and half of each was treated with TNF-α (10 ng/ml) and IFN-γ (50 U/ml) added directly to the growing media and both groups allowed to incubate for 36 hr at standard conditions."	"Trizol extraction of total RNA was performed according to the manufacturer's instructions."	"Approximately 5 micrograms of total RNA was processed to produce biotinylated cRNA targets using the older (ENZO) Affymetrix protocol"	"standard Affymetrix procedures"	"N78_control"	"GCRMA"	"Name: Michael Edwards;	Email: michael.edwards@ucdenver.edu;	Phone: 303-724-6054;	Fax: 303-724-6042;	Department: Pulmonary;	Institute: UC Denver;	Address: 12700 East 19th Avenue, Box C272;	City: Aurora;	State: CO;	Zip/postal_code: 80045;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM654nnn/GSM654540/GSM654540.CEL.gz"	54675	1	"download/GSM654540.CEL.gz"	"download/GSM654540.CEL"	4750747	13551955	64	1
517464	"N78 cell line, stimulated, biological rep3"	"GSM654541"	"GSE26594"	"GPL570"	"Public on Jan 13 2011"	"2011-01-12"	"2011-01-13"	"RNA"	"Human primary lung fibroblast from a control subject treated for 36 hr with TNF-α (10 ng/ml) and IFN-γ (50 U/ml)."	"Homo sapiens"	"treatment group: TNF-α and IFN-γ stimulated;	cell type: Human primary lung fibroblast"	"total RNA"	"biotin"	"Each cell line was divided into two groups and half of each was treated with TNF-α (10 ng/ml) and IFN-γ (50 U/ml) added directly to the growing media and both groups allowed to incubate for 36 hr at standard conditions."	"Trizol extraction of total RNA was performed according to the manufacturer's instructions."	"Approximately 5 micrograms of total RNA was processed to produce biotinylated cRNA targets using the older (ENZO) Affymetrix protocol"	"standard Affymetrix procedures"	"N78_stimulated"	"GCRMA"	"Name: Michael Edwards;	Email: michael.edwards@ucdenver.edu;	Phone: 303-724-6054;	Fax: 303-724-6042;	Department: Pulmonary;	Institute: UC Denver;	Address: 12700 East 19th Avenue, Box C272;	City: Aurora;	State: CO;	Zip/postal_code: 80045;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM654nnn/GSM654541/GSM654541.CEL.gz"	54675	1	"download/GSM654541.CEL.gz"	"download/GSM654541.CEL"	4656366	13551894	64	1
593848	"PMVECs treated with vehicle rep 1"	"GSM614501"	"GSE25014"	"GPL570"	"Public on Oct 13 2011"	"2010-10-29"	"2011-10-13"	"RNA"	"cultured lung endothelial cells"	"Homo sapiens"	"cell type: pulmonary microvascular endothelial cells;	treatment: control"	"total RNA"	"biotin"	"Cells were treated with freshly prepared heme (5 micromolar), every 48 hours for seven days"	"Trizol extraction of total RNA was performed according to the manufacturer's instructions."	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA."	"Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on a Human U 133 plus 2.0 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400."	"Gene expression data of PMVECs cultured for seven days in normal medium"	"Gene level expression index was generated using the Affymetrix MAS 5.0 software."	"Name: Tianwei Yu;	Department: Biostatistics;	Institute: Emory University;	Address: 1518 Clifton Rd NE;	City: Atlanta;	State: GA;	Zip/postal_code: 30322;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614501/GSM614501_Sample_1.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614501/GSM614501_Sample_1.CHP.gz"	54675	1	"download/GSM614501.CEL.gz"	"download/GSM614501.CEL"	5431487	13550648	64	1
593849	"PMVECs treated with vehicle rep2"	"GSM614502"	"GSE25014"	"GPL570"	"Public on Oct 13 2011"	"2010-10-29"	"2011-10-13"	"RNA"	"cultured lung endothelial cells"	"Homo sapiens"	"cell type: pulmonary microvascular endothelial cells;	treatment: control"	"total RNA"	"biotin"	"Cells were treated with freshly prepared heme (5 micromolar), every 48 hours for seven days"	"Trizol extraction of total RNA was performed according to the manufacturer's instructions."	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA."	"Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on a Human U 133 plus 2.0 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400."	"Gene expression data of PMVECs cultured for seven days in normal medium"	"Gene level expression index was generated using the Affymetrix MAS 5.0 software."	"Name: Tianwei Yu;	Department: Biostatistics;	Institute: Emory University;	Address: 1518 Clifton Rd NE;	City: Atlanta;	State: GA;	Zip/postal_code: 30322;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614502/GSM614502_Sample_2.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614502/GSM614502_Sample_2.CHP.gz"	54675	1	"download/GSM614502.CEL.gz"	"download/GSM614502.CEL"	5368916	13550920	64	1
593850	"PMVECs treated with vehicle rep 3"	"GSM614503"	"GSE25014"	"GPL570"	"Public on Oct 13 2011"	"2010-10-29"	"2011-10-13"	"RNA"	"cultured lung endothelial cells"	"Homo sapiens"	"cell type: pulmonary microvascular endothelial cells;	treatment: control"	"total RNA"	"biotin"	"Cells were treated with freshly prepared heme (5 micromolar), every 48 hours for seven days"	"Trizol extraction of total RNA was performed according to the manufacturer's instructions."	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA."	"Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on a Human U 133 plus 2.0 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400."	"Gene expression data of PMVECs cultured for seven days in normal medium"	"Gene level expression index was generated using the Affymetrix MAS 5.0 software."	"Name: Tianwei Yu;	Department: Biostatistics;	Institute: Emory University;	Address: 1518 Clifton Rd NE;	City: Atlanta;	State: GA;	Zip/postal_code: 30322;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614503/GSM614503_Sample_3.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614503/GSM614503_Sample_3.CHP.gz"	54675	1	"download/GSM614503.CEL.gz"	"download/GSM614503.CEL"	5402649	13551404	64	1
593851	"PMVECs treated with vehicle rep 4"	"GSM614504"	"GSE25014"	"GPL570"	"Public on Oct 13 2011"	"2010-10-29"	"2011-10-13"	"RNA"	"cultured lung endothelial cells"	"Homo sapiens"	"cell type: pulmonary microvascular endothelial cells;	treatment: control"	"total RNA"	"biotin"	"Cells were treated with freshly prepared heme (5 micromolar), every 48 hours for seven days"	"Trizol extraction of total RNA was performed according to the manufacturer's instructions."	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA."	"Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on a Human U 133 plus 2.0 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400."	"Gene expression data of PMVECs cultured for seven days in normal medium"	"Gene level expression index was generated using the Affymetrix MAS 5.0 software."	"Name: Tianwei Yu;	Department: Biostatistics;	Institute: Emory University;	Address: 1518 Clifton Rd NE;	City: Atlanta;	State: GA;	Zip/postal_code: 30322;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614504/GSM614504_Sample_4.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614504/GSM614504_Sample_4.CHP.gz"	54675	1	"download/GSM614504.CEL.gz"	"download/GSM614504.CEL"	5388831	13551012	64	1
593852	"PMVECs treated with vehicle rep 5"	"GSM614505"	"GSE25014"	"GPL570"	"Public on Oct 13 2011"	"2010-10-29"	"2011-10-13"	"RNA"	"cultured lung endothelial cells"	"Homo sapiens"	"cell type: pulmonary microvascular endothelial cells;	treatment: control"	"total RNA"	"biotin"	"Cells were treated with freshly prepared heme (5 micromolar), every 48 hours for seven days"	"Trizol extraction of total RNA was performed according to the manufacturer's instructions."	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA."	"Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on a Human U 133 plus 2.0 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400."	"Gene expression data of PMVECs cultured for seven days in normal medium"	"Gene level expression index was generated using the Affymetrix MAS 5.0 software."	"Name: Tianwei Yu;	Department: Biostatistics;	Institute: Emory University;	Address: 1518 Clifton Rd NE;	City: Atlanta;	State: GA;	Zip/postal_code: 30322;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614505/GSM614505_Sample_5.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614505/GSM614505_Sample_5.CHP.gz"	54675	1	"download/GSM614505.CEL.gz"	"download/GSM614505.CEL"	5261486	13550728	64	1
593853	"PMVECs treated with vehicle rep 6"	"GSM614506"	"GSE25014"	"GPL570"	"Public on Oct 13 2011"	"2010-10-29"	"2011-10-13"	"RNA"	"cultured lung endothelial cells"	"Homo sapiens"	"cell type: pulmonary microvascular endothelial cells;	treatment: control"	"total RNA"	"biotin"	"Cells were treated with freshly prepared heme (5 micromolar), every 48 hours for seven days"	"Trizol extraction of total RNA was performed according to the manufacturer's instructions."	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA."	"Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on a Human U 133 plus 2.0 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400."	"Gene expression data of PMVECs cultured for seven days in normal medium"	"Gene level expression index was generated using the Affymetrix MAS 5.0 software."	"Name: Tianwei Yu;	Department: Biostatistics;	Institute: Emory University;	Address: 1518 Clifton Rd NE;	City: Atlanta;	State: GA;	Zip/postal_code: 30322;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614506/GSM614506_Sample_6.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614506/GSM614506_Sample_6.CHP.gz"	54675	1	"download/GSM614506.CEL.gz"	"download/GSM614506.CEL"	5446678	13550700	64	1
593854	"PMVECs treated with 5 micromolar heme rep 1"	"GSM614507"	"GSE25014"	"GPL570"	"Public on Oct 13 2011"	"2010-10-29"	"2011-10-13"	"RNA"	"cultured lung endothelial cells"	"Homo sapiens"	"cell type: pulmonary microvascular endothelial cells;	treatment: heme"	"total RNA"	"biotin"	"Cells were treated with freshly prepared heme (5 micromolar), every 48 hours for seven days"	"Trizol extraction of total RNA was performed according to the manufacturer's instructions."	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA."	"Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on a Human U 133 plus 2.0 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400."	"Gene expression data of PMVECs cultured for seven days in five micromolar heme"	"Gene level expression index was generated using the Affymetrix MAS 5.0 software."	"Name: Tianwei Yu;	Department: Biostatistics;	Institute: Emory University;	Address: 1518 Clifton Rd NE;	City: Atlanta;	State: GA;	Zip/postal_code: 30322;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614507/GSM614507_Sample_7.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614507/GSM614507_Sample_7.CHP.gz"	54675	1	"download/GSM614507.CEL.gz"	"download/GSM614507.CEL"	5200679	13550864	64	1
593855	"PMVECs treated with 5 micromolar heme rep 2"	"GSM614508"	"GSE25014"	"GPL570"	"Public on Oct 13 2011"	"2010-10-29"	"2011-10-13"	"RNA"	"cultured lung endothelial cells"	"Homo sapiens"	"cell type: pulmonary microvascular endothelial cells;	treatment: heme"	"total RNA"	"biotin"	"Cells were treated with freshly prepared heme (5 micromolar), every 48 hours for seven days"	"Trizol extraction of total RNA was performed according to the manufacturer's instructions."	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA."	"Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on a Human U 133 plus 2.0 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400."	"Gene expression data of PMVECs cultured for seven days in five micromolar heme"	"Gene level expression index was generated using the Affymetrix MAS 5.0 software."	"Name: Tianwei Yu;	Department: Biostatistics;	Institute: Emory University;	Address: 1518 Clifton Rd NE;	City: Atlanta;	State: GA;	Zip/postal_code: 30322;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614508/GSM614508_Sample_8.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614508/GSM614508_Sample_8.CHP.gz"	54675	1	"download/GSM614508.CEL.gz"	"download/GSM614508.CEL"	5249667	13550912	64	1
593856	"PMVECs treated with 5 micromolar heme rep 3"	"GSM614509"	"GSE25014"	"GPL570"	"Public on Oct 13 2011"	"2010-10-29"	"2011-10-13"	"RNA"	"cultured lung endothelial cells"	"Homo sapiens"	"cell type: pulmonary microvascular endothelial cells;	treatment: heme"	"total RNA"	"biotin"	"Cells were treated with freshly prepared heme (5 micromolar), every 48 hours for seven days"	"Trizol extraction of total RNA was performed according to the manufacturer's instructions."	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA."	"Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on a Human U 133 plus 2.0 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400."	"Gene expression data of PMVECs cultured for seven days in five micromolar heme"	"Gene level expression index was generated using the Affymetrix MAS 5.0 software."	"Name: Tianwei Yu;	Department: Biostatistics;	Institute: Emory University;	Address: 1518 Clifton Rd NE;	City: Atlanta;	State: GA;	Zip/postal_code: 30322;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614509/GSM614509_Sample_9.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614509/GSM614509_Sample_9.CHP.gz"	54675	1	"download/GSM614509.CEL.gz"	"download/GSM614509.CEL"	5468578	13550712	64	1
593857	"PMVECs treated with 5 micromolar heme rep 4"	"GSM614510"	"GSE25014"	"GPL570"	"Public on Oct 13 2011"	"2010-10-29"	"2011-10-13"	"RNA"	"cultured lung endothelial cells"	"Homo sapiens"	"cell type: pulmonary microvascular endothelial cells;	treatment: heme"	"total RNA"	"biotin"	"Cells were treated with freshly prepared heme (5 micromolar), every 48 hours for seven days"	"Trizol extraction of total RNA was performed according to the manufacturer's instructions."	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA."	"Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on a Human U 133 plus 2.0 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400."	"Gene expression data of PMVECs cultured for seven days in five micromolar heme"	"Gene level expression index was generated using the Affymetrix MAS 5.0 software."	"Name: Tianwei Yu;	Department: Biostatistics;	Institute: Emory University;	Address: 1518 Clifton Rd NE;	City: Atlanta;	State: GA;	Zip/postal_code: 30322;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614510/GSM614510_Sample_10.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614510/GSM614510_Sample_10.CHP.gz"	54675	1	"download/GSM614510.CEL.gz"	"download/GSM614510.CEL"	5393690	13550917	64	1
593858	"PMVECs treated with 5 micromolar heme rep 5"	"GSM614511"	"GSE25014"	"GPL570"	"Public on Oct 13 2011"	"2010-10-29"	"2011-10-13"	"RNA"	"cultured lung endothelial cells"	"Homo sapiens"	"cell type: pulmonary microvascular endothelial cells;	treatment: heme"	"total RNA"	"biotin"	"Cells were treated with freshly prepared heme (5 micromolar), every 48 hours for seven days"	"Trizol extraction of total RNA was performed according to the manufacturer's instructions."	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA."	"Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on a Human U 133 plus 2.0 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400."	"Gene expression data of PMVECs cultured for seven days in five micromolar heme"	"Gene level expression index was generated using the Affymetrix MAS 5.0 software."	"Name: Tianwei Yu;	Department: Biostatistics;	Institute: Emory University;	Address: 1518 Clifton Rd NE;	City: Atlanta;	State: GA;	Zip/postal_code: 30322;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614511/GSM614511_Sample_11.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614511/GSM614511_Sample_11.CHP.gz"	54675	1	"download/GSM614511.CEL.gz"	"download/GSM614511.CEL"	5195235	13550945	64	1
593859	"PMVECs treated with 5 micromolar heme rep 6"	"GSM614512"	"GSE25014"	"GPL570"	"Public on Oct 13 2011"	"2010-10-29"	"2011-10-13"	"RNA"	"cultured lung endothelial cells"	"Homo sapiens"	"cell type: pulmonary microvascular endothelial cells;	treatment: heme"	"total RNA"	"biotin"	"Cells were treated with freshly prepared heme (5 micromolar), every 48 hours for seven days"	"Trizol extraction of total RNA was performed according to the manufacturer's instructions."	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA."	"Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on a Human U 133 plus 2.0 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400."	"Gene expression data of PMVECs cultured for seven days in five micromolar heme"	"Gene level expression index was generated using the Affymetrix MAS 5.0 software."	"Name: Tianwei Yu;	Department: Biostatistics;	Institute: Emory University;	Address: 1518 Clifton Rd NE;	City: Atlanta;	State: GA;	Zip/postal_code: 30322;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614512/GSM614512_Sample_12.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614512/GSM614512_Sample_12.CHP.gz"	54675	1	"download/GSM614512.CEL.gz"	"download/GSM614512.CEL"	5312984	13550853	64	1
593860	"PAECs treated with vehicle rep 1"	"GSM614513"	"GSE25014"	"GPL570"	"Public on Oct 13 2011"	"2010-10-29"	"2011-10-13"	"RNA"	"cultured lung endothelial cells"	"Homo sapiens"	"cell type: pulmonary artery endothelial cells;	treatment: control"	"total RNA"	"biotin"	"Cells were treated with freshly prepared heme (5 micromolar), every 48 hours for seven days"	"Trizol extraction of total RNA was performed according to the manufacturer's instructions."	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA."	"Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on a Human U 133 plus 2.0 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400."	"Gene expression data of PAECs cultured for seven days in normal medium"	"Gene level expression index was generated using the Affymetrix MAS 5.0 software."	"Name: Tianwei Yu;	Department: Biostatistics;	Institute: Emory University;	Address: 1518 Clifton Rd NE;	City: Atlanta;	State: GA;	Zip/postal_code: 30322;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614513/GSM614513_Sample_13.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614513/GSM614513_Sample_13.CHP.gz"	54675	1	"download/GSM614513.CEL.gz"	"download/GSM614513.CEL"	5350017	13550737	64	1
593861	"PAECs treated with vehicle rep 2"	"GSM614514"	"GSE25014"	"GPL570"	"Public on Oct 13 2011"	"2010-10-29"	"2011-10-13"	"RNA"	"cultured lung endothelial cells"	"Homo sapiens"	"cell type: pulmonary artery endothelial cells;	treatment: control"	"total RNA"	"biotin"	"Cells were treated with freshly prepared heme (5 micromolar), every 48 hours for seven days"	"Trizol extraction of total RNA was performed according to the manufacturer's instructions."	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA."	"Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on a Human U 133 plus 2.0 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400."	"Gene expression data of PAECs cultured for seven days in normal medium"	"Gene level expression index was generated using the Affymetrix MAS 5.0 software."	"Name: Tianwei Yu;	Department: Biostatistics;	Institute: Emory University;	Address: 1518 Clifton Rd NE;	City: Atlanta;	State: GA;	Zip/postal_code: 30322;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614514/GSM614514_Sample_14.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614514/GSM614514_Sample_14.CHP.gz"	54675	1	"download/GSM614514.CEL.gz"	"download/GSM614514.CEL"	5374468	13550561	64	1
593862	"PAECs treated with vehicle rep 3"	"GSM614515"	"GSE25014"	"GPL570"	"Public on Oct 13 2011"	"2010-10-29"	"2011-10-13"	"RNA"	"cultured lung endothelial cells"	"Homo sapiens"	"cell type: pulmonary artery endothelial cells;	treatment: control"	"total RNA"	"biotin"	"Cells were treated with freshly prepared heme (5 micromolar), every 48 hours for seven days"	"Trizol extraction of total RNA was performed according to the manufacturer's instructions."	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA."	"Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on a Human U 133 plus 2.0 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400."	"Gene expression data of PAECs cultured for seven days in normal medium"	"Gene level expression index was generated using the Affymetrix MAS 5.0 software."	"Name: Tianwei Yu;	Department: Biostatistics;	Institute: Emory University;	Address: 1518 Clifton Rd NE;	City: Atlanta;	State: GA;	Zip/postal_code: 30322;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614515/GSM614515_Sample_15.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614515/GSM614515_Sample_15.CHP.gz"	54675	1	"download/GSM614515.CEL.gz"	"download/GSM614515.CEL"	5304932	13550937	64	1
593863	"PAECs treated with vehicle rep 4"	"GSM614516"	"GSE25014"	"GPL570"	"Public on Oct 13 2011"	"2010-10-29"	"2011-10-13"	"RNA"	"cultured lung endothelial cells"	"Homo sapiens"	"cell type: pulmonary artery endothelial cells;	treatment: control"	"total RNA"	"biotin"	"Cells were treated with freshly prepared heme (5 micromolar), every 48 hours for seven days"	"Trizol extraction of total RNA was performed according to the manufacturer's instructions."	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA."	"Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on a Human U 133 plus 2.0 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400."	"Gene expression data of PAECs cultured for seven days in normal medium"	"Gene level expression index was generated using the Affymetrix MAS 5.0 software."	"Name: Tianwei Yu;	Department: Biostatistics;	Institute: Emory University;	Address: 1518 Clifton Rd NE;	City: Atlanta;	State: GA;	Zip/postal_code: 30322;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614516/GSM614516_Sample_16.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614516/GSM614516_Sample_16.CHP.gz"	54675	1	"download/GSM614516.CEL.gz"	"download/GSM614516.CEL"	5227317	13550797	64	1
593864	"PAECs treated with vehicle rep 5"	"GSM614517"	"GSE25014"	"GPL570"	"Public on Oct 13 2011"	"2010-10-29"	"2011-10-13"	"RNA"	"cultured lung endothelial cells"	"Homo sapiens"	"cell type: pulmonary artery endothelial cells;	treatment: control"	"total RNA"	"biotin"	"Cells were treated with freshly prepared heme (5 micromolar), every 48 hours for seven days"	"Trizol extraction of total RNA was performed according to the manufacturer's instructions."	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA."	"Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on a Human U 133 plus 2.0 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400."	"Gene expression data of PAECs cultured for seven days in normal medium"	"Gene level expression index was generated using the Affymetrix MAS 5.0 software."	"Name: Tianwei Yu;	Department: Biostatistics;	Institute: Emory University;	Address: 1518 Clifton Rd NE;	City: Atlanta;	State: GA;	Zip/postal_code: 30322;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614517/GSM614517_Sample_17.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614517/GSM614517_Sample_17.CHP.gz"	54675	1	"download/GSM614517.CEL.gz"	"download/GSM614517.CEL"	5176114	13550888	64	1
593865	"PAECs treated with vehicle rep 6"	"GSM614518"	"GSE25014"	"GPL570"	"Public on Oct 13 2011"	"2010-10-29"	"2011-10-13"	"RNA"	"cultured lung endothelial cells"	"Homo sapiens"	"cell type: pulmonary artery endothelial cells;	treatment: control"	"total RNA"	"biotin"	"Cells were treated with freshly prepared heme (5 micromolar), every 48 hours for seven days"	"Trizol extraction of total RNA was performed according to the manufacturer's instructions."	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA."	"Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on a Human U 133 plus 2.0 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400."	"Gene expression data of PAECs cultured for seven days in normal medium"	"Gene level expression index was generated using the Affymetrix MAS 5.0 software."	"Name: Tianwei Yu;	Department: Biostatistics;	Institute: Emory University;	Address: 1518 Clifton Rd NE;	City: Atlanta;	State: GA;	Zip/postal_code: 30322;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614518/GSM614518_Sample_18.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614518/GSM614518_Sample_18.CHP.gz"	54675	1	"download/GSM614518.CEL.gz"	"download/GSM614518.CEL"	5312752	13550805	64	1
593866	"PAECs treated with 5 micromolar heme rep 1"	"GSM614519"	"GSE25014"	"GPL570"	"Public on Oct 13 2011"	"2010-10-29"	"2011-10-13"	"RNA"	"cultured lung endothelial cells"	"Homo sapiens"	"cell type: pulmonary artery endothelial cells;	treatment: heme"	"total RNA"	"biotin"	"Cells were treated with freshly prepared heme (5 micromolar), every 48 hours for seven days"	"Trizol extraction of total RNA was performed according to the manufacturer's instructions."	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA."	"Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on a Human U 133 plus 2.0 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400."	"Gene expression data of PAECs cultured for seven days in five micromolar heme"	"Gene level expression index was generated using the Affymetrix MAS 5.0 software."	"Name: Tianwei Yu;	Department: Biostatistics;	Institute: Emory University;	Address: 1518 Clifton Rd NE;	City: Atlanta;	State: GA;	Zip/postal_code: 30322;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614519/GSM614519_Sample_19.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614519/GSM614519_Sample_19.CHP.gz"	54675	1	"download/GSM614519.CEL.gz"	"download/GSM614519.CEL"	5293113	13550857	64	1
593867	"PAECs treated with 5 micromolar heme rep 2"	"GSM614520"	"GSE25014"	"GPL570"	"Public on Oct 13 2011"	"2010-10-29"	"2011-10-13"	"RNA"	"cultured lung endothelial cells"	"Homo sapiens"	"cell type: pulmonary artery endothelial cells;	treatment: heme"	"total RNA"	"biotin"	"Cells were treated with freshly prepared heme (5 micromolar), every 48 hours for seven days"	"Trizol extraction of total RNA was performed according to the manufacturer's instructions."	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA."	"Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on a Human U 133 plus 2.0 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400."	"Gene expression data of PAECs cultured for seven days in five micromolar heme"	"Gene level expression index was generated using the Affymetrix MAS 5.0 software."	"Name: Tianwei Yu;	Department: Biostatistics;	Institute: Emory University;	Address: 1518 Clifton Rd NE;	City: Atlanta;	State: GA;	Zip/postal_code: 30322;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614520/GSM614520_Sample_20.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614520/GSM614520_Sample_20.CHP.gz"	54675	1	"download/GSM614520.CEL.gz"	"download/GSM614520.CEL"	5292547	13551264	64	1
593868	"PAECs treated with 5 micromolar heme rep 3"	"GSM614521"	"GSE25014"	"GPL570"	"Public on Oct 13 2011"	"2010-10-29"	"2011-10-13"	"RNA"	"cultured lung endothelial cells"	"Homo sapiens"	"cell type: pulmonary artery endothelial cells;	treatment: heme"	"total RNA"	"biotin"	"Cells were treated with freshly prepared heme (5 micromolar), every 48 hours for seven days"	"Trizol extraction of total RNA was performed according to the manufacturer's instructions."	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA."	"Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on a Human U 133 plus 2.0 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400."	"Gene expression data of PAECs cultured for seven days in five micromolar heme"	"Gene level expression index was generated using the Affymetrix MAS 5.0 software."	"Name: Tianwei Yu;	Department: Biostatistics;	Institute: Emory University;	Address: 1518 Clifton Rd NE;	City: Atlanta;	State: GA;	Zip/postal_code: 30322;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614521/GSM614521_Sample_21.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614521/GSM614521_Sample_21.CHP.gz"	54675	1	"download/GSM614521.CEL.gz"	"download/GSM614521.CEL"	5126881	13550905	64	1
593869	"PAECs treated with 5 micromolar heme rep 4"	"GSM614522"	"GSE25014"	"GPL570"	"Public on Oct 13 2011"	"2010-10-29"	"2011-10-13"	"RNA"	"cultured lung endothelial cells"	"Homo sapiens"	"cell type: pulmonary artery endothelial cells;	treatment: heme"	"total RNA"	"biotin"	"Cells were treated with freshly prepared heme (5 micromolar), every 48 hours for seven days"	"Trizol extraction of total RNA was performed according to the manufacturer's instructions."	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA."	"Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on a Human U 133 plus 2.0 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400."	"Gene expression data of PAECs cultured for seven days in five micromolar heme"	"Gene level expression index was generated using the Affymetrix MAS 5.0 software."	"Name: Tianwei Yu;	Department: Biostatistics;	Institute: Emory University;	Address: 1518 Clifton Rd NE;	City: Atlanta;	State: GA;	Zip/postal_code: 30322;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614522/GSM614522_Sample_22.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614522/GSM614522_Sample_22.CHP.gz"	54675	1	"download/GSM614522.CEL.gz"	"download/GSM614522.CEL"	5242304	13550845	64	1
593870	"PAECs treated with 5 micromolar heme rep 5"	"GSM614523"	"GSE25014"	"GPL570"	"Public on Oct 13 2011"	"2010-10-29"	"2011-10-13"	"RNA"	"cultured lung endothelial cells"	"Homo sapiens"	"cell type: pulmonary artery endothelial cells;	treatment: heme"	"total RNA"	"biotin"	"Cells were treated with freshly prepared heme (5 micromolar), every 48 hours for seven days"	"Trizol extraction of total RNA was performed according to the manufacturer's instructions."	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA."	"Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on a Human U 133 plus 2.0 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400."	"Gene expression data of PAECs cultured for seven days in five micromolar heme"	"Gene level expression index was generated using the Affymetrix MAS 5.0 software."	"Name: Tianwei Yu;	Department: Biostatistics;	Institute: Emory University;	Address: 1518 Clifton Rd NE;	City: Atlanta;	State: GA;	Zip/postal_code: 30322;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614523/GSM614523_Sample_23.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614523/GSM614523_Sample_23.CHP.gz"	54675	1	"download/GSM614523.CEL.gz"	"download/GSM614523.CEL"	5133616	13550733	64	1
593871	"PAECs treated with 5 micromolar heme rep 6"	"GSM614524"	"GSE25014"	"GPL570"	"Public on Oct 13 2011"	"2010-10-29"	"2011-10-13"	"RNA"	"cultured lung endothelial cells"	"Homo sapiens"	"cell type: pulmonary artery endothelial cells;	treatment: heme"	"total RNA"	"biotin"	"Cells were treated with freshly prepared heme (5 micromolar), every 48 hours for seven days"	"Trizol extraction of total RNA was performed according to the manufacturer's instructions."	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA."	"Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on a Human U 133 plus 2.0 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400."	"Gene expression data of PAECs cultured for seven days in five micromolar heme"	"Gene level expression index was generated using the Affymetrix MAS 5.0 software."	"Name: Tianwei Yu;	Department: Biostatistics;	Institute: Emory University;	Address: 1518 Clifton Rd NE;	City: Atlanta;	State: GA;	Zip/postal_code: 30322;	Country: USA"	"ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614524/GSM614524_Sample_24.CEL.gz;	ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM614nnn/GSM614524/GSM614524_Sample_24.CHP.gz"	54675	1	"download/GSM614524.CEL.gz"	"download/GSM614524.CEL"	5195384	13550897	64	1