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Sample GSM774962 Query DataSets for GSM774962
Status Public on Sep 02, 2011
Title EB Day3 Timepoint, TAF3 Control, replicate 2
Sample type SRA
Source name Embryoid body day 3, TAF3 control
Organism Mus musculus
Characteristics strain: D3
cell type: embryoid body day 3
genotype: TAF3 WT
timepoint: EB3
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
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)
SRA SRX091883
BioSample SAMN00709423
Named Annotation GSM774962_091120HHMI_6_eb3-2.bigwig

Supplementary file Size Download File type/resource
GSM774962_091120HHMI_6_eb3-2.bigwig 43.9 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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