|
Status |
Public on Sep 02, 2011 |
Title |
ES Timepoint, TAF3 KO, PE, replicate 1 |
Sample type |
SRA |
|
|
Source name |
Embryonic stem cells, TAF3 KO
|
Organism |
Mus musculus |
Characteristics |
strain: D3 cell type: embryonic stem cells genotype: TAF3 KO timepoint: ES
|
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 Paired-end reads.
|
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 |
SRX091888 |
BioSample |
SAMN00709428 |
Named Annotation |
GSM774967_100513_GA1_6_pe+1.bigwig |