|
| Status |
Public on Sep 02, 2011 |
| Title |
EB Day6 Timepoint, TAF3 Control, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Embryoid body day 6, TAF3 control
|
| Organism |
Mus musculus |
| Characteristics |
strain: D3
cell type: embryoid body day 6
genotype: TAF3 WT
timepoint: EB6
|
| Treatment protocol |
Samples were infected with lentiviral vectors expressing either anti-TAF3 (KO) or non-target (Control) shRNA constructs. ES samples were harvested after 72 hours, while EB samples were stimulated to differentiate (by withdrawl of LIF) and sampled either 3 or 6 days later.
|
| Growth protocol |
ES cells were cultured on 0.1% gelatin-coated plates in the absence of feeder cells. The ES cell medium was prepared by supplementing knockout DMEM (Invitrogen) with 15% FBS, 1mM glutamax, 0.1mM nonessential amino acids, 1mM sodium pyruvate, 0.1mM 2-mercapodhanol and 1000 units of LIF (Millipore).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
As per vendor protocol. Paired-end (PE) library insert (all) mean=240bp, sd=30bp.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
polyA RNA
Single read.
|
| Data processing |
Sequence reads were mapped to mm9 using TopHat v1.1.1 with default parameters.
|
| |
|
| Submission date |
Aug 08, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Devin Scannell |
| E-mail(s) |
devin.scannell@gmail.com
|
| Phone |
001-510-666-3640
|
| Organization name |
UC Berkeley
|
| Department |
QB3
|
| Lab |
Eisen
|
| Street address |
378 Stanley Hall #3220
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE30959 |
Control of Embryonic Stem Cell Lineage Commitment by Core Promoter Factor, TAF3 |
| GSE31271 |
Control of Embryonic Stem Cell Lineage Commitment by Core Promoter Factor, TAF3 (RNA-Seq data) |
|
| Relations |
| SRA |
SRX091887 |
| BioSample |
SAMN00709427 |
| Named Annotation |
GSM774966_100113HHMI_3_eb6-2.bigwig |
