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Sample GSM1122269 Query DataSets for GSM1122269
Status Public on Aug 07, 2013
Title VillinCreERT2+_Brg1fl/fl_Rep1
Sample type RNA
 
Source name Brg1 deficient
Organism Mus musculus
Characteristics tissue: Murine small intestine (jejunum)
genotype/variation: VillinCreERT2+_Brg1fl/fl
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using Trizol (Invitrogen), purified and on-column DNAse treated using Rneasy mini kit (Qiagen) according to manufacturer's protocol.
Label Cy3
Label protocol 100ng of total RNA was labelled using Illumina TotalPrepTM-96 RNA Amplification Kit (Ambion) according to manufacturer's protocol.
 
Hybridization protocol Samples were hybridised according to Illumina's Whole-Genome Gene Expression Direct Hybridization Assay Guide
Scan protocol Samples were scanned according to Illumina's Whole-Genome Gene Expression Direct Hybridization Assay Guide
Description Replicate_1
6816115008_G
Samples were enriched for epithelial cells by scraping epithelium off the muscle wall
Data processing 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
 
Submission date Apr 15, 2013
Last update date Aug 07, 2013
Contact name Aliaksei Holik
E-mail(s) sbiah2@cf.ac.uk
Organization name Cardiff University
Department School of Biosciences
Lab Prof Alan Clarke
Street address Museum Avenue
City Cardiff
ZIP/Postal code CF10 3AX
Country United Kingdom
 
Platform ID GPL6885
Series (1)
GSE46129 Transcriptome analysis of Brg1 deficient small intestinal epithelium in the context of normal and aberrant Wnt signalling

Data table header descriptions
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

Data table
ID_REF VALUE RAW_VALUE BEAD_STDERR Avg_NBEADS
ILMN_1250052 6.10505139279107 155.306931285755 56.1273009467422 66
ILMN_3122480 5.45087375029268 133.602720280303 37.1645766903333 41
ILMN_2599935 8.09724214032005 332.588873246729 128.678160272529 46
ILMN_2675543 5.40609894487751 132.446474130674 41.5970122452 48
ILMN_2686883 5.53425853846597 135.853957917488 31.0746367614577 34
ILMN_2751818 5.37413572676984 131.642729681617 40.0887844354751 35
ILMN_2728634 7.55334997440434 258.214757416192 94.9606138472202 47
ILMN_3040515 5.62865139686903 138.56433734319 38.1122123781175 53
ILMN_2711608 8.57967254603515 426.619669250974 166.138796787686 51
ILMN_1232875 5.38818293495001 131.993769227381 31.7360181187331 42
ILMN_1258507 5.54675372864152 136.202647726173 29.7464279809883 45
ILMN_2746142 4.7806041182133 119.539094708572 38.467009125587 35
ILMN_1252690 5.64589320756861 139.078843981876 38.3441050571069 52
ILMN_2655499 5.57863427887794 137.106098088581 35.4094551139709 36
ILMN_1252870 5.476708646033 134.286365916365 29.082667004196 46
ILMN_1248179 5.69394726296316 140.545667250753 50.1605554994375 44
ILMN_2649955 7.7775651415437 285.525125339749 99.8190069011332 45
ILMN_2628708 6.82712484826646 193.971966212344 59.8740845329713 45
ILMN_3024781 5.25073843305115 128.701467445717 39.4969875786015 48
ILMN_2705628 5.4589460871113 133.815018780882 33.7869869486678 43

Total number of rows: 25695

Table truncated, full table size 1672 Kbytes.




Supplementary data files not provided
Raw data included within Sample table
Processed data included within Sample table

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