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| Status |
Public on Oct 20, 2013 |
| Title |
ChIP-Seq H3K27ac HUVEC |
| Sample type |
SRA |
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| Source name |
primary HUVEC cells
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| Organism |
Homo sapiens |
| Characteristics |
treatment: no treat
experiment: ChIP-seq
antibody: H3K27ac (Abcam, ab4729)
restriction enzyme: no
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| Treatment protocol |
TNF-a (R&D Systems, 10 ng/mL, 1 hr) treatment were performed in IMR90 or HUVEC cells. Flavopiridol (Sigma, 1 μM for 1 hr) and IFN-γ (R&D, 50ng/mL for 2hrs) were performed in IMR90 cells. To find out primary TNF-α responsive genes, IMR90 cells were pre-treated with 5µg/mL of cycloheximide (sigma) for 30mins before TNF-α was added. Starvation and treatment of MCF7 cells with β-estradiol (Sigma, 100nM for 160min) were performed as described in previous literature (Hah, N. et al. Cell 145, 622-634, 2011); and LNCaP cells were starved and treated with 5α-dihydrotestosterone (DHT, 100nM, 4hr) as previously described(Wang, D. et al. Nature 474, 390-394, 2011)
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| Growth protocol |
IMR90 cells were grown as described in (Hawkins, R.D. et al. Cell Stem Cell 6, 479-91). MCF7 cells (ATCC), LNCaP cells (ATCC), and Human primary HUVEC cells (Lonza) were cultured following manufacturer’s instructions.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hi-C experiments were conducted in biological replicates using HindIII according to previous publication (Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-93 (2009).). ChIP-seq protocol can be found from http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf. GRO-seq experiments were performed according to previous publication (Wang, D. et al. Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature 474, 390-4 (2011).).
Libraries were prepared according to Illumina's instruction or cited literatures.
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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 |
The paired-end Hi-C reads were mapped to human genome hg18 using BOWTIE. Only first 36 bases were used for mapping when reads is longer. The two reads were mapped independently and then merged into pairs using in-house script. Duplicated read pairs from the same biological library were removed.
For GRO-seq, the first round of mapping used the first 36 bases; the unmapped reads were then mapped in two additional iterations using first 30 or 25 bases.
For ChIP-Seq, first 36 bases of each read were used for mapping.
RNA-seq data were analyzed using TOPHAT and CUFFLINK packages.
Genome_build: hg18
Supplementary_files_format_and_content: Mapped non-redundant reads for RNA-seq, GRO-seq and ChIP-seq are in BED format. Mapped non-redundant read pairs for Hi-C are in txt format.
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| Submission date |
Jun 05, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Fulai Jin |
| E-mail(s) |
fxj45@case.edu
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| Phone |
2163681811
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| Organization name |
Case Western Reserve University
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| Lab |
Fulai Jin
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| Street address |
10900 Euclid Avenue
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| City |
Cleveland |
| State/province |
OH - OHIO |
| ZIP/Postal code |
44106 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE43070 |
Genome-wide Analysis of Chromatin Interactions in Human Cells |
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| Relations |
| BioSample |
SAMN02191471 |
| SRA |
SRX294972 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1154045_H3K27ac.HUVEC.monoclonal.bed.gz |
130.0 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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