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Sample GSM1122266 Query DataSets for GSM1122266
Status Public on Aug 07, 2013
Title VillinCreERT2+_Apcfl/fl_Brg1+/+_Rep2
Sample type RNA
 
Source name Apc deficient
Organism Mus musculus
Characteristics tissue: Murine small intestine (jejunum)
genotype/variation: VillinCreERT2+_Apcfl/fl_Brg1+/+
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_D
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 5.40778091400847 126.302505345066 26.3535234690614 42
ILMN_3122480 4.98243930130308 115.728788229309 33.2701595360605 29
ILMN_2599935 9.59638155248947 839.611336640515 367.410373270164 38
ILMN_2675543 5.38085193887069 125.536816606622 40.0768080181802 52
ILMN_2686883 6.03504107283807 148.849404841605 49.7300668329795 43
ILMN_2751818 5.50175062499042 129.089094490011 37.8928852440102 48
ILMN_2728634 7.53719599957308 266.015005012572 99.8940152098628 49
ILMN_3040515 5.63148624710095 133.24686335555 36.7030186474088 52
ILMN_2711608 6.9029944508739 201.599849069898 73.3539239118457 43
ILMN_1232875 5.75853553737332 137.697206575609 41.9774806797879 41
ILMN_1258507 5.47690370908652 128.334554652987 37.0887071766419 54
ILMN_2746142 5.60957879394057 132.518295378305 36.2886310393751 30
ILMN_1252690 5.40230013241694 126.145507235292 30.5424625572334 51
ILMN_2655499 5.31206559878773 123.644579286914 32.0361977721788 49
ILMN_1252870 5.01961778289223 116.533930869802 30.0126546942429 39
ILMN_1248179 5.23541945071801 121.639622909682 20.9597900591742 31
ILMN_2649955 7.86234150595072 311.79281001968 132.84704745255 35
ILMN_2628708 8.42574579413749 420.178364615722 134.122926780317 47
ILMN_3024781 5.40003676066957 126.080846152295 40.2555126224221 46
ILMN_2705628 4.8588744547476 113.196924914858 25.992646853781 49

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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