Comment[ArrayExpressAccession]	E-GEOD-48397						
MAGE-TAB Version	1.1						
Public Release Date	2013-07-10						
Investigation Title	Expression data from (mouse) normal lung fibroblasts and carcinoma-associated fibroblasts						
Comment[Submitted Name]	Expression data from (mouse) normal lung fibroblasts and carcinoma-associated fibroblasts						
Experiment Description	Cancer-associated fibroblasts (CAFs) have been reported to support tumor progression by a variety of mechanisms. However, their role in the progression of non-small cell lung cancer (NSCLC) remains poorly defined. In addition, the extent to which specific proteins secreted by CAFs contribute directly to tumor growth is unclear. To study the role of CAFs in NSCLC, a cross-species functional characterization of mouse and human lung CAFs was performed, including gene expression analysis comparing normal mouse lung fibroblasts (NFs) and mouse lung CAFs to seek for differentially-expressed secreted proteins. Gene expression microarrays were used to identify transcriptomic changes between NFs and CAFs that may contribute to their different tumor-enhancing capacity. NFs and CAFs were grown in vitro for RNA extraction and hybridization on mouse 430_2 Affymetrix microarrays						
Term Source Name	ArrayExpress	EFO					
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl					
Person Last Name	Vaka	Sweet-Cordero	Vicent				
Person First Name	Dedeepya	Alejandro	Silvestre				
Person Email	dvaka@stanford.edu						
Person Affiliation	Stanford						
Person Address	Pediatrics, Stanford, 265 Campus Drive, Palo Alto, USA						
Person Roles	submitter						
Protocol Name	P-GSE48397-1	P-GSE48397-5	P-GSE48397-6	P-GSE48397-2	P-GSE48397-3	P-GSE48397-4	P-GSE48397-7
Protocol Description	The data were analyzed with RMA  using Affymetrix default analysis settings using Expression Console. On the RMA normalized data statistical test LIMMA is performed for D.E ID_REF =  VALUE = RMA signal	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).	cDNA synthesis, biotinylation of cRNA and hybridization to mouse Genechip 430A v2 containing 39,000 probes was performed according to the manufacturers instructions (Affymetrix, Santa Clara).	LFs and CAFs were trypsinized and plated at 10X6 cells/10cm dish, and grown overnight in 10% serum DMEM (including antibiotics).	LFs and CAFs were grown in 10% serum DMEM (including antibiotics) after isolation from mouse lungs and expanded for 10-14 days before being plated for RNA collection.	Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was cleaned up using Qiagen on-column Dnase treatment	GeneChips were scanned using Affymetrix scanner
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	disease						
Experimental Factor Type	disease						
Comment[SecondaryAccession]	GSE48397						
Comment[GEOReleaseDate]	2013-07-10						
Comment[ArrayExpressSubmissionDate]	2013-06-28						
Comment[GEOLastUpdateDate]	2013-07-11						
Comment[AEExperimentType]	transcription profiling by array						
Pubmed ID	22962265						
Publication DOI	10.1158/0008-5472.CAN-12-1097						
Publication Title	Cross-species functional analysis of cancer-associated fibroblasts identifies a critical role for CLCF1 and IL-6 in non-small cell lung cancer in vivo						
Publication Author List	Vicent S, Sayles LC, Vaka D, Khatri P, Gevaert O, Chen R, Zheng Y, Gillespie AK, Clarke N, Xu Y, Shrager J, Hoang CD, Plevritis S, Butte AJ, Sweet-Cordero EA						
SDRF File	E-GEOD-48397.sdrf.txt