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Sample GSM1122270 Query DataSets for GSM1122270
Status Public on Aug 07, 2013
Title VillinCreERT2+_Brg1fl/fl_Rep2
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_2
6816115008_H
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 5.78236321464103 171.303022352227 41.3595993504504 35
ILMN_3122480 5.43448478634481 160.044698700335 28.7516320743725 33
ILMN_2599935 7.88197172209262 343.916940301583 138.95675432371 35
ILMN_2675543 5.34156200013754 157.469006523953 30.3845720678161 45
ILMN_2686883 6.0662852412725 182.730248740671 35.6388839913732 28
ILMN_2751818 5.50834516871171 162.213593979429 39.7340861684538 47
ILMN_2728634 7.27365246028207 266.461017203356 75.0396932432208 53
ILMN_3040515 5.98739670114586 179.326496236672 46.6834960358598 40
ILMN_2711608 8.36923083310567 434.371177465531 160.16637826921 39
ILMN_1232875 5.63527090231084 166.20999442752 38.392709021549 43
ILMN_1258507 5.58393642327895 164.551242103443 48.4534935333059 42
ILMN_2746142 5.08131205185475 151.077987293875 29.918466779306 47
ILMN_1252690 5.89280498088174 175.48306295797 43.0294015096739 53
ILMN_2655499 5.92767077222564 176.870497690026 59.1053075247664 49
ILMN_1252870 5.02430718396772 149.825313025736 29.9847639876824 38
ILMN_1248179 5.66529040604432 167.207690503382 46.2742514066008 32
ILMN_2649955 7.51045620400341 292.804338021773 85.3397717488674 52
ILMN_2628708 6.72848077756571 219.986157294381 63.3335470253 54
ILMN_3024781 5.25058593940572 155.102859867361 34.947797450031 57
ILMN_2705628 5.26630365837322 155.501075328036 35.3536110012218 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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