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| Status |
Public on Jun 21, 2013 |
| Title |
Input2 |
| Sample type |
SRA |
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| Source name |
Genomic DNA
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| Organism |
Homo sapiens |
| Characteristics |
ChIP: input
treatment: N/A
cell line: C4-12/Flag.ER-beta
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
On 15-cm plates, C4-12/Flag.ERβ cells were treated with 10nM E2 for 1 hour then crosslinked with 1% formaldehyde. Cells were lysed with 1mL of ChIP-lysis buffer (50mM Tris pH 7.4, 100mM NaCl, 0.1% SDS, 1% Triton-X, 0.5% NP40, PICIII) and sonicated for 10 cycles, each of which was 10 seconds. The lysate was collected and incubated with 30uL Protein G Plus-Agarose (Santa Cruz) preimmuned with 10ug anti-Flag M2 antibodies (Sigma) to capture protein-DNA complex overnight in ChIP-lysis buffer. The Protein G beads were washed once with ChIP-wash buffer I (20mM Tris pH 8.1, 150mM NaCl, 0.1% SDS, 1% Triton X, 2mM EDTA), once with ChIP-wash buffer II (20mM Tris pH 8.1, 500mM NaCl, 0.1% SDS, 1% Triton X, 2mM EDTA), once with ChIP-wash buffer III (10mM Tris pH 8.1, 250mM LiCl, 1% NP40, 1% deoxycholate, 1mM EDTA), and twice with TE buffer. The protein-DNA complexes were eluted with ChIP-elution buffer (100mM NaHCO3, 1% SDS). The crosslinking was reversed by incubating samples at 65oC overnight. After treatment of RNase A and Proteinase K, the inputs and immunoprecipitated samples were extracted once with phenol/chloroform, once with chloroform, and precipitated in ethanol. The genomic DNA precipitate was suspended in 20uL nuclease-free water.
Illumina ChIP-seq kit
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
Additional input sample was required to identify FDR
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| Data processing |
Peak-calling software: QuEST
Genome_build: hg18
Supplementary_files_format_and_content: BED file
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| Submission date |
Jun 19, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Thien Le |
| E-mail(s) |
lethien@uchicago.edu
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| Organization name |
University of Chicago
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| Lab |
Geoffrey Greene
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| Street address |
929 E 57th St W325D
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
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| Platform ID |
GPL9115 |
| Series (2) |
| GSE48096 |
Mapping ERβ genomic binding sites reveals unique genomic features and identifies EBF1 as an ERβ interactor [ChIP-Seq] |
| GSE48161 |
Mapping ERβ genomic binding sites reveals unique genomic features and identifies EBF1 as an ERβ interactor |
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| Relations |
| BioSample |
SAMN02209910 |
| SRA |
SRX312103 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data not applicable for this record |
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