|
| Status |
Public on Apr 01, 2013 |
| Title |
Prdm14 knockout 2 |
| Sample type |
RNA |
| |
|
| Source name |
embryonic stem cell
|
| Organism |
Mus musculus |
| Characteristics |
cell type: embryonic stem cell
genetic background: C57BL/6
genotype: Prdm14 knockout
|
| Treatment protocol |
Biological replicates were collected from consecutive passages, no additional treatment was performed.
|
| Growth protocol |
Prdm14-null and wild-type control cells were grown in 2i culture conditions as described by Ying et al. (Nature, 2008)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with the RNeasy kit from Qiagen, followed by clean-up and DNase I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
|
| Label |
biotin
|
| Label protocol |
The Illumina Total-prep 96-RNA amplification kit from Ambion was used.
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Data processing |
The data were normalised using quantile normalisation with the lumi package in Bioconductor
not detected probes omitted (detection p-value where a probe is not detected in a sample if the p-value is above 0.01)
|
| |
|
| Submission date |
Mar 26, 2013 |
| Last update date |
Apr 01, 2013 |
| Contact name |
Charles Bradshaw |
| Organization name |
University of Cambridge
|
| Department |
Gurdon Institute
|
| Street address |
Tennis Court Road
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 1QN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL6887 |
| Series (2) |
| GSE45507 |
Genome-wide identification of genes differentially expressed between wild-type and Prdm14-deficient ES cells grown in 2i culture conditions. |
| GSE45509 |
Prdm14 |
|
