Comment[ArrayExpressAccession]	E-GEOD-47369
MAGE-TAB Version	1.1				
Public Release Date	2013-06-09
Investigation Title	Targeting BCL-2 with the BH3 mimetic ABT-199 in ER-positive breast cancer				
Comment[Submitted Name]	Targeting BCL-2 with the BH3 mimetic ABT-199 in ER-positive breast cancer
Experiment Description	A bank of human breast tumor xenografts was established by serial passage of primary breast tumor fragments in the cleared mammary fat pads of immuno-compromised NOD-SCID-IL2Rgammac-/- mice. The expression profiles from four different tumors (23T, 315T, 50T and 838T) were classified using diagonal discriminant analysis. The training data set consisted of 1992 samples from Curtis et al. (2012, PMID: 22522925); class labels were based on tumor subtype information provided (Basal-like, Luminal A, Luminal B, HER2-enriched and Normal breast-like). Total RNA obtained from xenograft tumors from different patients have been profiled on the Illumina HT-12 BeadChip platform.				
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	Ritchie	Ritchie			
Person First Name	Matthew	Matthew			
Person Mid Initials		E			
Person Email	mritchie@wehi.edu.au				
Person Affiliation	The Walter and Eliza Hall Institute of Medical Research				
Person Address	Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria, Australia				
Person Roles	submitter				
Protocol Name	P-GSE47369-1	P-GSE47369-3	P-GSE47369-4	P-GSE47369-2	P-GSE47369-5
Protocol Description	The GenomeStudio software (version 1.9.0) was used to convert the signal on the array into a TXT file for analysis. The data were then calibrated and quantile normalized using the neqc method of Shi et al. (2010) [PMID:20929874]. This analysis was carried out in R (version 2.15.2) using the limma package (version 4.15.9). ID_REF =  VALUE = Calibrated, quantile normalized and log2 transformed intensity	Human total RNA was quality ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol. A total of 500ng was labelled using the Ambion Total Prep RNA amplification kit (Cat. No. IL1791). The quantity of labelled product was ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol. A total of 750ng of labelled cRNA was then prepared for hybridisation to the Sentrix Human- HT12v4 BeadChip by preparing a probe cocktail (cRNA @ 0.05ug/ul) that includes GEX-HYB Hybridisation Buffer (supplied with the BeadChip).	A total hybridisation volume of 15ul is prepared for each sample and 15ul loaded into a single array on the Sentrix Human-HT12v4 BeadChip. The chip is hybridised at 58C for 16 hours in an oven with a rocking platform. After hybridisation, the chip is washed using the appropriate protocols as outlined in the Illumina manual. Upon completion of the washing, the chips are then coupled with Cy3 and scanned in the illumina BeadArray Reader.	RNA was extracted using Invitrogen Trizol Reagent in accordance with the prescribed protocol provided with the kit. DNase treatment was performed using the QIAGEN RNase-free DNase Set prior to RNA purification using the QIAGEN RNAeasy kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.	Arrays were scanned in the Illumina BeadArray Reader.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	TUMOR ID				
Experimental Factor Type	tumor id				
Comment[SecondaryAccession]	GSE47369				
Comment[GEOReleaseDate]	2013-06-09				
Comment[ArrayExpressSubmissionDate]	2013-05-24				
Comment[GEOLastUpdateDate]	2013-06-09				
Comment[AEExperimentType]	transcription profiling by array				
SDRF File	E-GEOD-47369.sdrf.txt