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Sample GSM1122267 Query DataSets for GSM1122267
Status Public on Aug 07, 2013
Title VillinCreERT2-_Rep1
Sample type RNA
 
Source name Cre-negative (control)
Organism Mus musculus
Characteristics tissue: Murine small intestine (jejunum)
genotype/variation: VillinCreERT2-
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_E
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 6.00017193990311 190.708894112963 32.9282251380134 36
ILMN_3122480 5.38329354081814 165.900405085615 41.7982532348304 51
ILMN_2599935 8.46442944267662 512.816065310783 131.473337065596 37
ILMN_2675543 5.28840965610472 162.940242809817 35.3985535008383 49
ILMN_2686883 5.35242984386763 164.916103269305 38.1416276446191 41
ILMN_2751818 5.20145393993051 160.393024882281 30.7459716664948 37
ILMN_2728634 6.70625646057205 235.721265885152 61.806255506218 55
ILMN_3040515 5.1440387389936 158.793276031986 29.112427073431 33
ILMN_2711608 7.41039672051977 308.892432872563 96.1266744762226 49
ILMN_1232875 5.31747488384581 163.826436316668 35.3070642373422 45
ILMN_1258507 5.39050752515424 166.133522090856 37.7577866419949 31
ILMN_2746142 4.98840273241586 154.763418994333 34.9205211743125 36
ILMN_1252690 5.80379709721627 181.635298186451 39.9008266942945 41
ILMN_2655499 5.38499019896183 165.955127210981 42.268940307007 44
ILMN_1252870 5.56875899605208 172.279632490854 35.3792521837981 34
ILMN_1248179 4.93379828820386 153.449331098796 37.0739938916894 37
ILMN_2649955 7.18237945208153 281.193897402169 84.9481401124217 41
ILMN_2628708 7.66032485848361 344.729250052551 119.273433974349 48
ILMN_3024781 5.21810969352519 160.869125916497 39.5787942647911 32
ILMN_2705628 5.25235064158563 161.865312783261 26.5634940342434 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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