|
| 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 |
| E-mail(s) |
[email protected]
|
| 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) |
|
| Relations |
| SRA |
SRX091897 |
| BioSample |
SAMN00709438 |
