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Sample GSM774945 Query DataSets for GSM774945
Status Public on Sep 02, 2011
Title TBP/PolII Mock IP, ES Cells
Sample type SRA
Source name Embryonic stem cells, TBP/PolII mock
Organism Mus musculus
Characteristics strain: D3
cell type: embryonic stem cells
chip antibody: mock IgG
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 genomic DNA
Extraction protocol Chromatin Immunoprecipitation (ChIP) was performed according to (Boyer et al., 2006) with minor modifications. Briefly, cross-linked ES cell (D3) chromatin was sheared using the Covaris S2 system to a size range of 100bp~400bp. Immunoprecipitation was conducted with either a specific antibody (custom-made except for anti-TBP (Abcam ab62126)) or mock IgG-conjugated Protein A (rabbit and guinea pig) or G (mouse) Sepharose beads (GE Healthcare). The reverse cross-linking was performed at 70oC overnight. After RNAse A and Proteinase K treatment, sample was deproteinized with UltraPure Phenol:Chloroform:Isoamyl Alcohol (Invitrogen) and further purified with the Qiaquick PCR purification kit (Qiagen).

About 10ng of ChIP-enriched DNA (DNA concentration was measured with Quant-iT PicoGreen dsDNA Reagent (invitrogen)) was converted to ChIP-Seq library using the ChIP-Seq DNA Sample Prep Kit (Illumina; IP-102-1001).
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Data processing Sequence reads were mapped to mm9 using vendor software (Eland) 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
GSE31270 Control of Embryonic Stem Cell Lineage Commitment by Core Promoter Factor, TAF3 (ChIP-Seq data)
SRA SRX091897
BioSample SAMN00709438

Supplementary file Size Download File type/resource
GSM774945_100527_GA4_s_3_export.txt.gz 1.2 Gb (ftp)(http) TXT
GSM774945_100527_GA4_s_4_export.txt.gz 1.2 Gb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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