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Sample GSM1122277 Query DataSets for GSM1122277
Status Public on Aug 07, 2013
Title VillinCreERT2+_Brg1fl/fl_Rep4
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_4
6816115033_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 5.89017702120233 175.345245126666 48.0258276437812 40
ILMN_3122480 5.76750577336283 170.980115331685 42.7118039371925 27
ILMN_2599935 7.69124869286851 308.383580511253 67.2957601961477 40
ILMN_2675543 6.05191134999713 181.697710246356 35.8087438284991 61
ILMN_2686883 5.98910807650105 179.146100024217 48.7630784867053 39
ILMN_2751818 5.60195159091933 165.647476236819 42.8737292052088 43
ILMN_2728634 6.04714753971725 181.500247508698 45.5245615539164 46
ILMN_3040515 5.22262923570959 155.506791562454 22.9083508805666 29
ILMN_2711608 6.05181474625762 181.693699486305 49.7578588965915 43
ILMN_1232875 5.79724302649338 172.004471280123 40.9260252672335 45
ILMN_1258507 5.74052166824023 170.068684666666 29.2163641480539 33
ILMN_2746142 5.10012635169895 152.761247394223 24.7252351298397 34
ILMN_1252690 5.98071967600369 178.813619618518 37.0616862326651 45
ILMN_2655499 5.50827553672251 162.890233308391 36.9008226944038 45
ILMN_1252870 6.07803207850522 182.792091683529 34.8354771766182 29
ILMN_1248179 5.98505445655075 178.985190532766 37.0398796610709 37
ILMN_2649955 6.07666756091626 182.734430760508 35.4938955735632 47
ILMN_2628708 6.0591658345913 181.999667754317 45.2475378412132 45
ILMN_3024781 5.75063913578839 170.408423068212 39.1412220487687 43
ILMN_2705628 6.09305863645778 183.430693572592 48.2799317467163 30

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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