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| Status |
Public on Dec 11, 2015 |
| Title |
PolII_S2P-ChIP + JQ1 |
| Sample type |
SRA |
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| Source name |
human LX2 cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: human hepatic stellate cells
cell line: LX-2
chip antibody: PolII-s2p
treatment: JQ1 (500nM)
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| Treatment protocol |
LX-2 cells were treated with DMSO (0.1%) or JQ1(500nM) for 16 hrs.
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| Growth protocol |
LX-2 cells were cultured as described by Xu, L., Hui, A.Y., Albanis, E., Arthur, M.J., O'Byrne, S.M., Blaner, W.S., Mukherjee, P., Friedman, S.L., and Eng, F.J. (2005). Human hepatic stellate cell lines, LX-1 and LX-2: new tools for analysis of hepatic fibrosis. Gut 54, 142-151.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Standard Illumina DNA library construction
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Alignment: Sequence reads were obtained using the Illumina CASAVA v1.8.2. Reads were aligned against the human hg18 reference genome (NCBI Build 36.1) using the Bowtie aligner. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 200 bp to create summary windows.
Peaks: Peak detection and Superenhancer identification were performed with the HOMER software suite (http://biowhat.ucsd.edu/homer/).
Genome_build: hg18
Supplementary_files_format_and_content: bowtie files are alignments made from fastq files with the Bowtie aligner; bedGraph files were generated on Homer and can be visualized on the UCSC genome browser; peak and superenhancer files were generated using Homer.
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| Submission date |
Jun 19, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Ruth T Yu |
| Organization name |
Salk Institute
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| Department |
Gene Expression Lab
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| Lab |
Ronald Evans
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| Street address |
10010 N Torrey Pines Rd
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE58680 |
Super-Enhancer-mediated Control of Liver Fibrosis by BET Bromodomain Proteins |
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| Relations |
| BioSample |
SAMN02867609 |
| SRA |
SRX612509 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1416814_PolII_S2P_JQ1_LX2.ucsc.bedGraph.gz |
35.8 Mb |
(ftp)(http) |
BEDGRAPH |
| GSM1416814_PolII_S2P_JQ1_peaks.txt.gz |
353.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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