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Sample GSM1122271 Query DataSets for GSM1122271
Status Public on Aug 07, 2013
Title VillinCreERT2+_Apcfl/fl_Brg1fl/fl_Rep3
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_3
6816115033_A
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 5.90381537581497 161.164871757359 35.0619196310625 34
ILMN_3122480 5.52123775009285 147.803218304446 37.6322692385753 35
ILMN_2599935 9.42187549197518 760.805014484806 224.845583263623 33
ILMN_2675543 5.93986947185476 162.616365154417 43.5211299657245 44
ILMN_2686883 5.84848538507978 159.006692422502 49.5799127504816 40
ILMN_2751818 5.11830214446614 137.078892511608 33.7565042553747 45
ILMN_2728634 6.6416649895531 199.459365455853 42.0851757822545 37
ILMN_3040515 5.95141510398246 163.08889538801 42.5690049160385 44
ILMN_2711608 7.04107332473253 229.965916366318 83.6519929285172 42
ILMN_1232875 5.30735347475737 141.739625559414 31.6347087957219 46
ILMN_1258507 5.79067561723651 156.838443554295 43.7366566852388 47
ILMN_2746142 4.98942150836627 134.233768751923 29.4228582059697 26
ILMN_1252690 5.80504776973326 157.369410631803 41.2556681517824 29
ILMN_2655499 5.6193519832821 150.899885822217 45.5499696421722 49
ILMN_1252870 5.72796171311706 154.582411709921 35.1646897340955 28
ILMN_1248179 4.89803449787237 132.364715698462 29.1875049499553 42
ILMN_2649955 7.36582765154492 261.811477121708 86.5372722514904 51
ILMN_2628708 7.15209869818857 240.057046874879 84.4434515199515 48
ILMN_3024781 5.77043380039493 156.09953671244 43.1876488555937 46
ILMN_2705628 5.45111077558123 145.715355830388 19.2471056943187 32

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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