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Sample GSM1122273 Query DataSets for GSM1122273
Status Public on Aug 07, 2013
Title VillinCreERT2+_Apcfl/fl_Brg1+/+_Rep3
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_3
6816115033_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 5.71876882922236 168.433937742347 49.3578202150135 37
ILMN_3122480 5.38564283097329 156.57977669876 25.8544149800131 27
ILMN_2599935 9.75868329445549 1056.34007652728 309.189743770478 34
ILMN_2675543 5.79877541924272 171.712057801978 44.272193403557 31
ILMN_2686883 6.03102521062674 182.325227629097 58.5947138449859 35
ILMN_2751818 5.37166882340939 156.139812462341 31.7139773237379 45
ILMN_2728634 7.26988749809395 279.392582935399 83.7267023746191 43
ILMN_3040515 4.90220817807456 143.581837118979 26.3084326694393 24
ILMN_2711608 6.63186719112825 219.194840502777 64.9858394569975 40
ILMN_1232875 5.35818724093671 155.719368305554 32.0530224794016 33
ILMN_1258507 5.94931890426472 178.395299046469 65.326161372261 33
ILMN_2746142 4.94158265942118 144.48546983854 37.165425915767 32
ILMN_1252690 5.53412699147833 161.527423582657 36.8796066230351 28
ILMN_2655499 5.31330611157524 154.347631879381 33.4319685278718 45
ILMN_1252870 5.33483036935693 155.00017515603 20.9771374077843 28
ILMN_1248179 5.13349973945136 149.260294075517 25.1376858699561 27
ILMN_2649955 7.29458698779775 282.30093517854 84.299456392708 51
ILMN_2628708 7.93621942950608 378.263396334754 130.3740749388 36
ILMN_3024781 4.8456158343255 142.325433279312 32.1666780826606 42
ILMN_2705628 5.82812585277044 172.960927574162 41.9788614948209 46

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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