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Sample GSM1122276 Query DataSets for GSM1122276
Status Public on Aug 07, 2013
Title VillinCreERT2+_Brg1fl/fl_Rep3
Sample type RNA
 
Source name Brg1 deficient
Organism Mus musculus
Characteristics tissue: Murine small intestine (jejunum)
genotype/variation: VillinCreERT2+_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_G
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 6.12751536858497 200.639691259471 45.8293264997866 39
ILMN_3122480 5.26806137509149 166.356363976736 28.4229078289502 32
ILMN_2599935 7.41767164000945 311.029721028549 106.144761839419 36
ILMN_2675543 5.79401453437598 184.876384587041 43.2279799520758 39
ILMN_2686883 5.97356732978361 192.909690678359 61.9293617628949 34
ILMN_2751818 5.48769095564066 173.279967430081 37.799511612784 41
ILMN_2728634 6.50445667103278 223.442663634794 61.6368128717418 38
ILMN_3040515 5.57454482978314 176.322049057256 46.3777497488564 39
ILMN_2711608 8.0001700804717 403.925247218823 128.672013916505 41
ILMN_1232875 5.35205185279719 168.880521353002 25.2495656828414 37
ILMN_1258507 5.65977153701245 179.490437302763 35.0019387592444 39
ILMN_2746142 5.64213625467527 178.819391840696 47.663354299509 37
ILMN_1252690 5.80043729222245 185.146840906414 46.0390671118695 54
ILMN_2655499 5.42079399533471 171.058515953701 45.2756568291096 42
ILMN_1252870 5.78700461146933 184.582573575483 57.5739648706306 31
ILMN_1248179 5.27932332762982 166.686356340075 34.3944080068556 47
ILMN_2649955 7.36317565136042 304.107086723037 101.222651248685 41
ILMN_2628708 6.53050093174891 225.249188058015 61.6373266391189 43
ILMN_3024781 5.27536048945354 166.569945589773 42.6239632273698 33
ILMN_2705628 5.55505928579943 175.623551546935 29.2745917701445 38

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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