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Sample GSM1122265 Query DataSets for GSM1122265
Status Public on Aug 07, 2013
Title VillinCreERT2+_Apcfl/fl_Brg1+/+_Rep1
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_1
6816115008_C
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 5.77206933679907 127.671752501 34.6598315939896 50
ILMN_3122480 5.41353552231761 117.984114137498 33.3292567834595 28
ILMN_2599935 9.75242744831832 778.336772036727 302.587637877144 49
ILMN_2675543 4.58291392433564 102.947485316919 21.2199523544449 44
ILMN_2686883 5.10369350398482 111.346257587542 34.7061383721792 33
ILMN_2751818 5.40711379394775 117.831592189582 31.9624343961494 40
ILMN_2728634 7.56028486514359 235.679079236437 80.5240887108908 50
ILMN_3040515 5.49240403536424 119.913703195556 33.4355435057545 30
ILMN_2711608 6.41930775717942 152.593824406503 48.6612697843725 41
ILMN_1232875 5.91891340286987 132.38847080413 50.7710202882891 39
ILMN_1258507 4.12788939961129 97.7168870147652 20.7587401297032 35
ILMN_2746142 5.45174560024559 118.905799941335 40.6822676312798 25
ILMN_1252690 5.19776440219534 113.213259554621 25.7649875201732 50
ILMN_2655499 5.174991999334 112.750084807904 34.6727426920694 45
ILMN_1252870 5.631529823206 123.585430565335 33.9190025725939 25
ILMN_1248179 5.02097842513558 109.802135364732 24.0294519473742 23
ILMN_2649955 7.07362964022271 192.153599769022 69.8987397255624 28
ILMN_2628708 7.1710237922138 199.730556184916 68.806068194051 42
ILMN_3024781 6.03026772164627 136.299196970707 44.0583556319568 44
ILMN_2705628 5.25898647504245 114.495296536299 30.1591744752474 45

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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