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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 02, 2011 |
| Title |
TAF1 Mock IP, ES Cells |
| Sample type |
SRA |
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| Source name |
Embryonic stem cells, TAF1 mock
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| Organism |
Mus musculus |
| Characteristics |
strain: D3
cell type: embryonic stem cells
chip antibody: mock IgG
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| 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).
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| 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).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Data processing |
Sequence reads were mapped to mm9 using vendor software (Eland) with default parameters.
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| Submission date |
Aug 08, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Devin Scannell |
| E-mail(s) |
devin.scannell@gmail.com
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| Phone |
001-510-666-3640
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| Organization name |
UC Berkeley
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| Department |
QB3
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| Lab |
Eisen
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| Street address |
378 Stanley Hall #3220
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| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
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| 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) |
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| Relations |
| SRA |
SRX091895 |
| BioSample |
SAMN00709436 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM774943_100525_GA2_s_7_export.txt.gz |
1.2 Gb |
(ftp)(http) |
TXT |
| GSM774943_100525_GA2_s_8_export.txt.gz |
1.2 Gb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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