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Sample GSM1122275 Query DataSets for GSM1122275
Status Public on Aug 07, 2013
Title VillinCreERT2-_Rep4
Sample type RNA
 
Source name Cre-negative (control)
Organism Mus musculus
Characteristics tissue: Murine small intestine (jejunum)
genotype/variation: VillinCreERT2-
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_F
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 5.95675735352012 176.900328890988 41.1084516235479 45
ILMN_3122480 5.2293942679536 151.164117831435 34.6432240060905 41
ILMN_2599935 8.51805078153066 495.420004628284 185.373986180736 33
ILMN_2675543 4.35085934616616 133.248649246383 17.8316554690259 23
ILMN_2686883 5.60635617835978 162.886980559252 28.1312704869975 27
ILMN_2751818 5.64755024969568 164.363518160479 38.7587887822347 42
ILMN_2728634 6.54515091769431 209.621882963387 56.8081425790209 40
ILMN_3040515 5.31488061054797 153.560910722301 36.6279301564912 39
ILMN_2711608 6.93014112126945 239.501761604677 67.3812407600046 38
ILMN_1232875 5.42997293878158 157.020251486152 35.7522740134248 48
ILMN_1258507 5.66775824119182 165.103392683525 42.9076090346011 29
ILMN_2746142 5.14029717714561 148.812571079534 36.2358557936603 38
ILMN_1252690 5.72435241053354 167.23145385516 39.2133977522682 42
ILMN_2655499 5.14012969176199 148.808285809794 35.729829788184 42
ILMN_1252870 5.41740549755355 156.628961745517 24.9790451637475 31
ILMN_1248179 5.38885663409945 155.752641866664 31.3729713522908 32
ILMN_2649955 6.97900106562464 243.896251693146 74.1687790011695 47
ILMN_2628708 6.75153443091123 224.646636881765 55.2369382745852 39
ILMN_3024781 4.96128549367801 144.5045553585 33.1974416927707 51
ILMN_2705628 5.33362998361606 154.105831998584 33.0850774817452 47

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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