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Sample GSM1122264 Query DataSets for GSM1122264
Status Public on Aug 07, 2013
Title VillinCreERT2+_Apcfl/fl_Brg1fl/fl_Rep2
Sample type RNA
 
Source name Brg1-Apc deficient
Organism Mus musculus
Characteristics tissue: Murine small intestine (jejunum)
genotype/variation: VillinCreERT2+_Apcfl/fl_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_2
6816115008_B
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 6.19171150931667 190.419214778869 52.5057095565056 41
ILMN_3122480 5.58380789147294 167.335793002927 42.8310890996491 38
ILMN_2599935 9.50171323058795 788.961169014755 241.247002519738 29
ILMN_2675543 5.78788559998889 174.029447805216 40.9973449043433 50
ILMN_2686883 5.68918685391848 170.673969555737 40.1793896637747 30
ILMN_2751818 5.48450348027991 164.405403056811 40.1316184036308 31
ILMN_2728634 7.19055782533118 257.434322519103 84.819793804477 41
ILMN_3040515 5.58331611659221 167.320778873611 36.8742433467265 32
ILMN_2711608 6.88163206465253 231.579019624378 63.8280840050774 49
ILMN_1232875 5.97695278246322 181.134663387807 47.2205045467124 36
ILMN_1258507 6.36088224905984 198.770507602906 58.5040538782413 44
ILMN_2746142 4.74540474463121 147.914640526942 43.6432310031951 40
ILMN_1252690 5.79235117746575 174.186757590028 25.9839345862371 39
ILMN_2655499 5.61439671296397 168.279809843852 34.9409069227433 28
ILMN_1252870 6.00764922865611 182.378636675758 57.4630705291561 33
ILMN_1248179 5.57327990233585 167.015482930479 37.9797139075219 51
ILMN_2649955 7.07760259870448 247.333018629932 56.4005258152276 44
ILMN_2628708 6.41125027592127 201.452100432452 52.3010676581196 38
ILMN_3024781 5.8232383074731 175.288252014012 52.8573643846399 44
ILMN_2705628 5.1344896442056 155.545118844157 37.7461085967876 39

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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