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Sample GSM1122274 Query DataSets for GSM1122274
Status Public on Aug 07, 2013
Title VillinCreERT2-_Rep3
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_3
6816115033_E
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 6.06420951125986 187.841285476356 53.7106414983207 47
ILMN_3122480 5.1746376239699 153.290021560512 32.6594912182369 37
ILMN_2599935 8.23750438160351 451.31988644263 119.762181645089 43
ILMN_2675543 5.37160765994765 159.21925737083 34.8884753355001 36
ILMN_2686883 5.92531615243246 180.951478402288 55.8577462000827 34
ILMN_2751818 5.2017927774842 154.060193521134 32.2181711573041 40
ILMN_2728634 6.51876848703765 215.640932686339 50.8448298650361 37
ILMN_3040515 5.58986845586276 166.806687531215 44.370152700512 42
ILMN_2711608 7.25502681298666 284.12551511136 97.2836620883023 45
ILMN_1232875 5.39253733952323 159.898139072943 34.7401677774431 45
ILMN_1258507 5.6086786885016 167.515873167554 36.2660217160684 44
ILMN_2746142 5.08668857939066 150.892718189879 26.8234626745701 28
ILMN_1252690 5.77469879081985 174.192635463962 46.874747176206 37
ILMN_2655499 4.9999158740058 148.666286396512 32.1363674716013 43
ILMN_1252870 5.34447340960265 158.353643924173 31.892571333801 37
ILMN_1248179 5.61564429161619 167.780844574825 35.2145548419896 32
ILMN_2649955 7.18522102456599 276.032764593025 81.7625173315587 43
ILMN_2628708 6.93221030282222 249.774098628158 73.2957758599997 44
ILMN_3024781 4.86646209343261 145.492710587583 26.2186243620198 34
ILMN_2705628 5.44389932225737 161.606439257189 40.2956937071342 51

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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