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Sample GSM1122268 Query DataSets for GSM1122268
Status Public on Aug 07, 2013
Title VillinCreERT2-_Rep2
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_2
6816115008_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 5.58299991724643 174.21076073739 36.8422840595738 52
ILMN_3122480 5.08096867848211 158.67829951635 26.1894480725216 35
ILMN_2599935 8.55051062825065 534.604059919346 174.520089543916 27
ILMN_2675543 5.06100088526069 158.165233149209 32.0409937936944 42
ILMN_2686883 5.77486937774774 181.727190834479 40.0405536273799 34
ILMN_2751818 5.59196891414559 174.540308195239 38.4729547329865 28
ILMN_2728634 6.86357937757916 249.730075541504 70.7960324813762 51
ILMN_3040515 5.54696317367117 172.907111719536 31.7961831117421 29
ILMN_2711608 7.20355291431655 283.834760855833 82.4568123118621 40
ILMN_1232875 5.17289437997517 161.133971784181 33.1066743458209 42
ILMN_1258507 5.36360919991407 166.755500469231 36.3544340741883 26
ILMN_2746142 5.33494984715656 165.862615248545 38.6315169028689 42
ILMN_1252690 6.56548463260519 225.771393873012 65.1146232617781 56
ILMN_2655499 5.31964552714998 165.39301630849 44.8339570742398 36
ILMN_1252870 5.23906537365872 163.000926320894 31.2258703761534 42
ILMN_1248179 5.3922744320796 167.666472912579 36.9302735585575 34
ILMN_2649955 7.3415317827508 300.138086944443 65.5732201247995 33
ILMN_2628708 7.18480474190391 281.737405933334 65.8988081529827 51
ILMN_3024781 5.89825771003164 187.116321091566 62.1672015799079 27
ILMN_2705628 5.64610309057783 176.573424873811 45.8219640521801 42

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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