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Sample GSM1122263 Query DataSets for GSM1122263
Status Public on Aug 07, 2013
Title VillinCreERT2+_Apcfl/fl_Brg1fl/fl_Rep1
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_1
6816115008_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 5.66924402640265 178.614948893729 25.3032239640542 31
ILMN_3122480 5.27494859608765 165.394936126768 40.5902863912517 22
ILMN_2599935 9.24475679833103 782.165651766522 231.323678440544 39
ILMN_2675543 5.54256225031859 173.968034877134 47.6412059459645 31
ILMN_2686883 5.81182065010581 184.356640871083 47.412952029753 39
ILMN_2751818 5.34656759513915 167.535884810975 35.6677156476797 40
ILMN_2728634 6.86490961007413 249.937947721387 62.1699079303647 20
ILMN_3040515 5.82226955928389 184.800155378011 44.7658841003294 47
ILMN_2711608 6.71272537080963 237.265422993272 58.4905286633275 38
ILMN_1232875 4.79379357011977 153.462590734075 35.7229115674942 30
ILMN_1258507 5.18789879384021 162.931681729749 34.9613913235801 31
ILMN_2746142 4.84092930995539 154.46392787698 28.6598630889118 35
ILMN_1252690 5.58453087983589 175.462579366047 32.3171980554068 45
ILMN_2655499 5.15793320687643 162.117515157492 38.3311235775541 31
ILMN_1252870 5.41629779144406 169.724917820087 28.1105963129426 26
ILMN_1248179 5.4496153785639 170.808768763397 44.2701274547737 34
ILMN_2649955 7.5230259564829 323.103172564236 104.28980622083 33
ILMN_2628708 6.86366168773231 249.828502899591 55.0353714294087 27
ILMN_3024781 4.40797587197836 146.385339380554 26.4785464816114 28
ILMN_2705628 5.47618047862101 171.691056110474 35.7195552578421 44

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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