Comment[ArrayExpressAccession]	E-GEOD-45195
MAGE-TAB Version	1.1						
Public Release Date	2013-08-06
Investigation Title	Exon arrays from HT-29, MCF10A, and MDA-MB-436 cells						
Comment[Submitted Name]	Exon arrays from HT-29, MCF10A, and MDA-MB-436 cells
Experiment Description	Expression data from HT-29 cells treated with IFN-γ for 24 hr, MCF10A cells, and MDA-MB-436 cells. Total RNA was isolated with the RNeasy Mini Kit (Qiagen). Sense-strand cDNA synthesis, terminal labeling, and hybridization were performed using Ambion WT Expression Kit (Applied Biosystems, P/N 4425209).						
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	Kang	Kang	Jensen	Hatch	Janes		
Person First Name	Byong	Byong	Karin	Jaime	Kevin		
Person Mid Initials	Ha	H	J	A	A		
Person Email	bhk3j@virginia.edu						
Person Affiliation	University of Virginia						
Person Address	Department of Biomedical Engineering, University of Virginia, 415 Lane Road, MR5-Rm. 2225, Charlottesville, VA, USA						
Person Roles	submitter						
Protocol Name	P-GSE45195-1	P-GSE45195-5	P-GSE45195-6	P-GSE45195-2	P-GSE45195-3	P-GSE45195-4	P-GSE45195-7
Protocol Description	Exon array data were analyzed with the R package JETTA. The gene expression index for each transcript cluster was calculated for the core probe set after median-GC background correction and normalization by median scaling. Background correction was performed by combining the exon array data with an earlier dataset of 178 human cell lines (GSE29682). probe group file: HuEx-1_0-st-v2.r2.pgf meta-probeset file: HuEx-1_0-st-v2.na33.hg19.core.mps ID_REF =  VALUE = Gene expression indices from JETTA	Biotin-labeled cRNA was prepared using the GeneChip WT Terminal Labeling Kit (Affymetrix) according to the manufacturer's protocols.	Samples were hybridized, stained, and washed using the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix) according to the manufacturer's protocols.	HT-29 cells were treated with 200 U ml-1 IFN-γ (Roche) for 24 hr.	HT-29 cells were cultured in McCoy's 5A medium with 10% FBS and 5% CO2. MCF10A cells were cultured in DMEM/F12 medium with 5% horse serum, 20 ng/ml EGF, 500 ng/ml hydrocortisone, 100 ng/ml cholera toxin, and 10 µg/ml insulin. MDA-MB-436 cells were cultured in L-15 medium with 10% FBS without CO2.	Total RNA was isolated with the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocols.	GeneChip Scanner 3000 7G (Affymetrix)
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	CELL LINE	CELL TYPE					
Experimental Factor Type	cell line	cell type					
Comment[SecondaryAccession]	GSE45195						
Comment[GEOReleaseDate]	2013-08-06						
Comment[ArrayExpressSubmissionDate]	2013-03-15						
Comment[GEOLastUpdateDate]	2013-08-08						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-45195.sdrf.txt