Comment[ArrayExpressAccession]	E-GEOD-54830
MAGE-TAB Version	1.1										
Public Release Date	2014-07-01
Investigation Title	Up-regulation of IFN-related genes in BRCA2-/- cells										
Comment[Submitted Name]	Up-regulation of IFN-related genes in BRCA2-/- cells
Experiment Description	Microarray-based expression profiling of BRCA2 knockout and isogenic wild type HCT116 human colorectal cancer cells One way ANOVA, single factor comparison of wild type and BRCA2 knockout cells, three CEL files for wild type, three CEL files for BRCA2 knockout										
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	McKinney	Xu	Xian	Vire	McKinney	Wong	Wei	Tong	Kouzarides	Caldas	Aparicio
Person First Name	Steven	Hong	Jian	Emmanuelle	Steven	Jason	Vivien	Rebecca	Tony	Carlos	Samuel
Person Email	smckinney@bccrc.ca										
Person Affiliation	British Columbia Cancer Agency										
Person Phone	604-675-8000										
Person Fax	604-675-8218										
Person Address	Molecular Oncology, British Columbia Cancer Agency, 675 West 10th Ave, Vancouver, BC, Canada										
Person Roles	submitter										
Protocol Name	P-GSE54830-1	P-GSE54830-5	P-GSE54830-6	P-GSE54830-2	P-GSE54830-3	P-GSE54830-4	P-GSE54830-7				
Protocol Description	The microarray data were analyzed using the oneChannelGUI package of the R statistical programming language (R version 2.11.1, R Development Core Team, 2010).  Raw intensity calls were normalized using quantile normalization (Bolstad et al 2003) and probeset summarization (core plus extended) undertaken with RMA (Irizarry et al 2003) probe group file: HuEx-1_0-st-v2.r2.pgf meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps ID_REF =  VALUE = Matrix table:  log2 gene level expression values from Affymetrix dabg (apt/bin/apt-probeset-summarize -a dabg).  oneChannelGUI table:  R programming language oneChannelGUI output	Samples with a resulting total RNA of 1 M-5g or greater and with a RNA integrity number (RIN) of 7.0 or greater were used and the whole transcript sense target labeling procedure followed the Affymetrix protocol, including the RiboMinusM-bM-^DM-" rRNA removal step. Three technical replicates were compared for each of the genotypes (HCT116 homozygous BRCA2-/- and isogenic wild type) for a total of six experiments.	Labelled RNA was probed on Human Exon Array 1.0 ST chips (Affymetrix, Santa Clara, California) for gene expression analysis and scanned at the CTAG Facility of the British Columbia Cancer Agency, Vancouver, BC, Canada.	The wild-type HCT116 line was obtained from ATCC (ATCC number CCL-247). Isogenic BRCA2-deficient lines were generated by sequentially targeting both alleles of the BRCA2 gene by homologous recombination (J. Xian and C. Caldas).	Cells were incubated in 6mm plates. HCT116 human colon carcinoma cells were maintained in McCoyM-bM-^@M-^Ys 5A media (Gibco, Invitrogen) supplemented with 10 % fetal bovine serum (Sigma-Aldrich, St. Louis, MO) and 20 mM L-glutamine, at 37 C in a humidified atmosphere containing 5% CO2.	Total RNA was isolated from frozen HCT116 samples (three wild type and three BRCA2-/-) using QIAzolM-bM-^DM-" lysis reagent (Qiagen, Maryland, USA). The tissues were homogenized in 800 M-5L QIAzol and transferred to Phase Lock Gel tubes (2 mL, heavy) (Eppendorf AG, Hamburg, Germany) to which 200 M-5L chloroform was added. Samples were centrifuged and the aqueous phase was removed and transferred to a new tube with an equal volume of isopropanol. After centrifugation, the supernatant was removed from the precipitated RNA pellets, and the pellets were washed with 70% ethanol. The air-dried RNA was dissolved in RNase/DNase free water and stored frozen at -80 M-0C. Total RNA samples were analyzed on a NanoDrop (Thermo Fisher Scientific, Waltham, MA) spectrophotometer to determine RNA quality and concentration. One M-5L of the RNA (was adjusted within a range of 25-500 ng/M-5L) was analyzed on the Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany) using the RNA 6000 Nano kit.	Array scanning was performed according to the manufacturer's instructions (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	GENOTYPE										
Experimental Factor Type	genotype										
Comment[SecondaryAccession]	GSE54830										
Comment[GEOReleaseDate]	2014-07-01										
Comment[ArrayExpressSubmissionDate]	2014-02-10										
Comment[GEOLastUpdateDate]	2014-07-02										
Comment[AEExperimentType]	transcription profiling by array										
SDRF File	E-GEOD-54830.sdrf.txt