|
| Status |
Public on Dec 08, 2015 |
| Title |
R EtOH rep3 hyb1 |
| Sample type |
RNA |
| |
|
| Source name |
ESCs
|
| Organism |
Mus musculus |
| Characteristics |
treatment: EtOH
hyb number: 1
|
| Treatment protocol |
Tamoxifen was added at 1uM for 36h to induce knockout
|
| Growth protocol |
All cells were grown in Knockout DMEM with 15%FBS, Pen/Strep, L-glutamine and Non-essential amino acids. ESCs were also grown in Lif and 2i (GSKi and MEKi).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with the standard Trizol protocol
|
| Label |
biotin
|
| Label protocol |
Standard Illumina protocol
|
| |
|
| Hybridization protocol |
Standard Illumina protocol - a subset of the RNA was hybed on two separate chips at different times and used as such on Sample Network (see hyb#)
|
| Scan protocol |
Standard Illumina protocol
|
| Data processing |
Using RGui, the data was processed by Sample Network (ref) and subsequently quantile normalized. Differential gene expression was performed using the limma package, with a cutoff of adjusted p-value < 0.05.
|
| |
|
| Submission date |
Jun 09, 2014 |
| Last update date |
Dec 08, 2015 |
| Contact name |
Raga Krishnakumar |
| E-mail(s) |
raga.krishnakumar@gmail.com
|
| Organization name |
UCSF
|
| Lab |
Blelloch
|
| Street address |
912E RMB, 35 Medical Center Way
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL6885 |
| Series (2) |
| GSE58317 |
Foxd3 binding at enhancers controls developmental timing of gene expression by regulation of histone acetylation [expression array] |
| GSE58408 |
Foxd3 binding at enhancers controls developmental timing of gene expression by regulation of histone acetylation |
|
