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| Status |
Public on Jun 10, 2017 |
| Title |
HCC70_STAT3_Rep1 |
| Sample type |
SRA |
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| Source name |
HCC70 cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HCC70
treatment: ethanol
chip-seq antibody: anti-STAT3 (Santa Cruz Biotechnology, sc-482)
cell type: HCC70 (Human Tnm Stage Iiia, Grade 3, Primary Ductal Carcinoma)
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| Treatment protocol |
HCC70, MDA-MB-231, MDA-MB-468, MDA-MB-157, HCC1143 were treated with Ethanol, STAT3 pooled siRNA (L-003544-00-0005, GE Healthcare, Logan, UT), Nontargeting siRNA (D-001810-01-05, GE Healthcare, Logan, UT)
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| Growth protocol |
TNBC cells were grown under recommended growth conditions
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq was performed as previously described (Reddy et al. Molecular Cell 2013). RNA-seq was performed as previously outlned (Gertz et al. 2012)
Illumina Single End for ChIP-seq, Illumina Paired End for RNA-seq
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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 and ChIP input control FASTQ files were aligned to hg19 female genome using Bowtie
Peak Calling was performed using MACS peak caller
Genome_build: hg19 female
Supplementary_files_format_and_content: [.bedgraph] Chromosome number, start position, stop position, dataValue
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| Submission date |
Aug 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Joy Agee |
| E-mail(s) |
jagee@hudsonalpha.org
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| Phone |
2059945492
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| Organization name |
HudsonAlpha Institute for Biotechnology
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| Street address |
601 Genome Way
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| City |
Huntsville |
| State/province |
AL |
| ZIP/Postal code |
35806 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE85579 |
Genomic Regulation of Invasion by STAT3 in Triple Negative Breast Cancer |
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| Relations |
| BioSample |
SAMN05572266 |
| SRA |
SRX2020842 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2278004_HCC70_STAT3_Rep1.bedgraph.gz |
77.6 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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