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| Status |
Public on Oct 26, 2016 |
| Title |
MCF7+EtOH ChIP-seq input |
| Sample type |
SRA |
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| Source name |
MCF7+EtOH ChIP-seq input
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| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7
cell type: Human breast cancer cell line
treated with: ethanol (vehicle)
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| Treatment protocol |
For vehicle experiment, instead of estradiol, EtOH was added.
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| Growth protocol |
The human breast cancer MCF7 cells (ATCC # HTB-22) were grown in DMEM supplemented with 10% fetal bovine serum (FBS).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-seq, cells were crosslinked using 1% formaldehyde and lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq: Libraries were barcoded (NEXTflex™ DNA Barcodes) (Bio Scientific, Austin, TX).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
ChIP-seq reads were aligned to hg19 genome assembly using bwa.
For ChIP-seq, Sole-Search (alpha=0.0001, FDR=0.0001, peakmergedistance=0, histoneblurlength=1200) was used to call peaks.
Genome_build: hg19
Supplementary_files_format_and_content: For ChIP-seq, tab-delimited text files include location of peaks
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| Submission date |
May 24, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Suhn K Rhie |
| Organization name |
University of Southern California
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| Street address |
1450 Biggy Street
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90089 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE78913 |
Tracing Enhancer Networks using Epigenetic Traits (TENET) |
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| Relations |
| BioSample |
SAMN05170559 |
| SRA |
SRX1795469 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data not provided for this record |
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