|
| Status |
Public on Jan 31, 2011 |
| Title |
SV40 immortalized MEF Tdg heterozygous rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Mouse embryonic fibroblasts - TDG heterozygotes, SV40 immortalized
|
| Organism |
Mus musculus |
| Characteristics |
clone: 4
genotype: Tdg+/-
cell type: embryonic fibroblast
|
| Growth protocol |
Cells were grown in DMEM 10% FCS 1x Penicillin/Streptomycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cell pellets stored in RNA later using the RNeasy Mini Kit (Qiagen)
|
| Label |
biotin-streptavidin R-phycoerythrin
|
| Label protocol |
13 µg of total RNA were used to generate cDNA with the SuperScript double-Stranded cDNA Synthesis kit (Invitrogen) followed by in vitro transcription and labelling reactions performed with the MEGA Script T7 Kit (Ambion) supplemented with 1.5 mM Bio-11-CTP and Bio-16-UTP (Enzo Life Sciences).
|
| |
|
| Hybridization protocol |
15 µg of fragmented cRNA were hybridized to Mouse Genome 430A 2.0 Arrays (Affymetrix) according to the manufacturers protocol.
|
| Scan protocol |
Arrays were scanned with a Affymetrix Scanner 3000 7G using the Microarray Suite software
|
| Description |
n/a
|
| Data processing |
Scanned images were processed with the Microarray Suite software. Data was normalized by robust multi-array average (RMA) expression measure 'rma()' and detection calls and p-values were calculated by 'mas5calls()'. Statistical analysis were performed with R / Bioconductor using the package affy and libraries contained therein, in particular limma.
|
| |
|
| Submission date |
Mar 09, 2010 |
| Last update date |
Feb 01, 2011 |
| Contact name |
Fredy Siegrist |
| E-mail(s) |
fredy.siegrist@dkf.unibe.ch
|
| Organization name |
University Hospital Bern
|
| Department |
Department of Nephrology
|
| Lab |
KKL D830
|
| Street address |
Freiburgstrasse 15
|
| City |
Bern |
| ZIP/Postal code |
3010 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL339 |
| Series (1) |
| GSE20693 |
Effects of Tdg deficiency on overall transcription in mouse embryonic fibroblasts and during cell differentiation |
|
