|
| Status |
Public on Jan 01, 2008 |
| Title |
Undifferentiated Dicer +/- (D4) ES cell line replicate_2 |
| Sample type |
RNA |
| |
|
| Source name |
Embryonic stem cell
|
| Organism |
Mus musculus |
| Characteristics |
Undifferentiated Dicer +/- ES cell line, passage 20
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Absolutely RNA Miniprep Kit (Stratagene)
|
| Label |
biotinylated cRNA
|
| Label protocol |
cRNA was produced by in vitro transcription (IVT) by T7 RNA polymerase, using the Affymetrix IVT kit as per manufacturer’s instructions.
|
| |
|
| Hybridization protocol |
20 µg of biotinylated cRNA was fragmented by heating in the presence of Mg2+ (as per Affymetrix’s instructions) and 15 µg of fragmented cRNA was hybridized to Mouse MOE430 v2.0 GeneChips™
|
| Scan protocol |
standard Affymetrix procedures
|
| Description |
ES cells heterozygous for Dicer_date of analysis 16082006
|
| Data processing |
Quality control and background normalization were performed using Refiner from Genedata AG (Basel, Switzerland). All arrays were condensed together using the GC-RMA algorithm with quantile normalization composed of 100 bins using Genedata’s Refiner application. Per chip normalization was performed by scaling the median of the genes called present (detection p-value < 0.04) to a value of 500. Per chip normalized data are referred to as “raw” expression values.
|
| |
|
| Submission date |
Feb 27, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Lasse Sinkkonen |
| E-mail(s) |
[email protected]
|
| Organization name |
Friedrich Miescher Institute
|
| Street address |
Maulbeerstrasse 66
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE7141 |
mRNA expression analysis of undifferentiated Dicer +/- (D4) and Dicer -/- (27H10) embryonic cell lines |
|
| Relations |
| Reanalyzed by |
GSE119085 |
