|
| Status |
Public on Aug 07, 2013 |
| Title |
VillinCreERT2+_Apcfl/fl_Brg1+/+_Rep2 |
| 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_2
6816115008_D
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 |
|
