Comment[ArrayExpressAccession]	E-GEOD-46129
MAGE-TAB Version	1.1				
Public Release Date	2013-08-07
Investigation Title	Transcriptome analysis of Brg1 deficient small intestinal epithelium in the context of normal and aberrant Wnt signalling				
Comment[Submitted Name]	Transcriptome analysis of Brg1 deficient small intestinal epithelium in the context of normal and aberrant Wnt signalling
Experiment Description	Brg1 has been reported to act as a trans-activator for the Wnt pathway by interacting with beta-catenin. Given this interaction and the crucial role Wnt signalling plays in the intestinal homeostasis, we aimed to investigate the effect of Brg1 loss on gene expression in normal and Wnt activated small intestinal epithelium. We used VillinCreERT2 Cre recombinase and loxP targeted allels of Brg1 and Apc to generate 4 cohorts of conditional knock-out mice: Cre-negative controls (n=4), Brg1 deficient (n=4), Apc deficient (n=3) and double Brg1-Apc deficient (n=4). All mice were induced by 4x80mg/kg daily injections of Tamoxifen. Epithelium enriched (gut scrapes) samples of small intestine (jejunum) were collected at day 4 post induction. Loss of Brg1 expression in the small intestinal epithelium at this time point was confirmed by immunohistochemistry.				
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	Holik				
Person First Name	Aliaksei				
Person Email	sbiah2@cf.ac.uk				
Person Affiliation	Cardiff University				
Person Address	School of Biosciences, Cardiff University, Museum Avenue, Cardiff, United Kingdom				
Person Roles	submitter				
Protocol Name	P-GSE46129-1	P-GSE46129-3	P-GSE46129-4	P-GSE46129-2	P-GSE46129-5
Protocol Description	The bead-level data were preprocessed using BASH (Cairns et al. (2008) Bioinformatics 24(24):2921-2), a function from the beadarray package (Dunning et al (2007) Bioinformatics 23(16):2183-4) in Bioconductor, and normalised using variance stabilising data transformation (vsn) method (Huber et al. (2002) Bioinformatics 18: S96–S104) from the beadarray package ID_REF = Illumina probe identifier for the platform VALUE = normalized signal intensity RAW_VALUE = raw signal intensity BEAD_STDERR = the standard error of the probe measurements Avg_NBEADS = Number of beads for the probe	100ng of total RNA was labelled using Illumina TotalPrepTM-96 RNA Amplification Kit (Ambion) according to manufacturer's protocol.	Samples were hybridised according to Illumina's Whole-Genome Gene Expression Direct Hybridization Assay Guide	Total RNA was isolated using Trizol (Invitrogen), purified and on-column DNAse treated using Rneasy mini kit (Qiagen) according to manufacturer's protocol.	Samples were scanned according to Illumina's Whole-Genome Gene Expression Direct Hybridization Assay Guide
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	GENOTYPE				
Experimental Factor Type	genotype				
Comment[SecondaryAccession]	GSE46129				
Comment[GEOReleaseDate]	2013-08-07				
Comment[ArrayExpressSubmissionDate]	2013-04-17				
Comment[GEOLastUpdateDate]	2013-08-07				
Comment[AEExperimentType]	transcription profiling by array				
SDRF File	E-GEOD-46129.sdrf.txt