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Sample GSM1122272 Query DataSets for GSM1122272
Status Public on Aug 07, 2013
Title VillinCreERT2+_Apcfl/fl_Brg1fl/fl_Rep4
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_4
6816115033_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 5.58689018065887 167.53692125385 30.8065820701796 26
ILMN_3122480 6.0161257122042 185.418036671733 46.0002566216414 34
ILMN_2599935 9.18838915720981 742.17316099555 170.680086419395 40
ILMN_2675543 5.62736421079966 169.00519551111 48.0957970246346 39
ILMN_2686883 5.78097241336099 174.967730203148 39.8883952858778 30
ILMN_2751818 5.63154392588466 169.159181132611 35.6448190106795 31
ILMN_2728634 6.35193154956271 203.626498399045 43.9675131957435 35
ILMN_3040515 5.41096222986701 161.612157990784 32.6762405574429 44
ILMN_2711608 6.59781464297222 219.919141339366 51.8510778279342 35
ILMN_1232875 5.73778893430729 173.226898010266 40.0760641989895 46
ILMN_1258507 5.67838162370498 170.915576103871 24.2247455466471 29
ILMN_2746142 4.92919132186431 148.639682153116 26.9539614723719 41
ILMN_1252690 5.69596604099443 171.589838733642 40.4963010906321 54
ILMN_2655499 4.98994654046064 150.04734458132 27.5295834395714 22
ILMN_1252870 5.43133149412564 162.261764562699 37.3176111821137 28
ILMN_1248179 5.75104390526473 173.755709681911 52.0685349750495 32
ILMN_2649955 6.99930091149886 253.279627124 67.7393964059452 44
ILMN_2628708 6.83720673658592 238.685267980083 71.0037928673821 41
ILMN_3024781 5.46776725410468 163.44686167801 41.0718624692468 39
ILMN_2705628 5.68619630418474 171.214210979817 41.8930552272368 48

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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