|
| Status |
Public on Jan 31, 2011 |
| Title |
ES knockout rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Embryonic stem cells, TDG knock-out
|
| Organism |
Mus musculus |
| Characteristics |
differentiation stage: embryonal stem
differentiation time days: 0
genotype: Tdg-/-
cell type: Embryonic stem cells
|
| Treatment protocol |
differentiation: embryoid body formation in absence of feeder cells and LIF, induction of differentiation with 5 µM all-trans retinoic acid and further growth in DMEM- F12 nutrient mixture (1:1) + 1x N2 supplement
|
| Growth protocol |
ES cells: grown in DMEM, 15 % heat inactivated FCS, LIF (1,000 U/ml), 1x nonessential amino acids, 1 mM sodium pyruvate, 2 mM L-glutamine and 90 µM β-mercaptoethanol
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using TRIZOL.
|
| Label |
Cy3
|
| Label protocol |
Starting with 500 ng / sample of total RNA, total RNAs was transcribed and labeled with Illumina(r) TotalPrep RNA Amplification Kit (Ambion). cRNA was quantified with QuantIT (Invitrogen) against ribosomal RNA standard (Invitrogen).
|
| |
|
| Hybridization protocol |
1500 ng cRNA was hybridized on two Illumina MouseWG-6 v2 slides acording to the manufacturers protocol. Biological replicates were distributed among both slides.
|
| Scan protocol |
Fluorescent signals were imaged by laser scanning using the Illumina iScan system.
|
| Description |
n/a
|
| Data processing |
The data was processed with Illumina genome studio software (gene expression module 1.0.6) with no background correction or normalization. VST (variance stabilization) transformation 'lumiT()', quantile normalization 'lumiN(, method = quantile)' and statistical analysis were performed with R (2.9.0) / Bioconductor using the package lumi (1.10.1) and libraries contained therein, in particular limma (2.16.4).
|
| |
|
| Submission date |
Mar 09, 2010 |
| Last update date |
Jan 31, 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 |
GPL6887 |
| Series (1) |
| GSE20693 |
Effects of Tdg deficiency on overall transcription in mouse embryonic fibroblasts and during cell differentiation |
|
