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Status |
Public on Jun 21, 2013 |
Title |
Veh_ChIP |
Sample type |
SRA |
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Source name |
ChIP'ed DNA
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Organism |
Homo sapiens |
Characteristics |
ChIP: anti-Flag M2 (Sigma) treatment: Vehicle 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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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 |
SAMN02209912 |
SRA |
SRX312101 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1168433_GEOarchive_TL_Veh_ERbeta_ChIPseq_calls.bed.gz |
241 b |
(ftp)(http) |
BED |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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