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| Status |
Public on Feb 08, 2017 |
| Title |
V389 H3K4me1 ChIP Seq |
| Sample type |
SRA |
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| Source name |
CRC cell line
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| Organism |
Homo sapiens |
| Characteristics |
tissue: colorectal cancer cell line
cell line: V389
chip antibody: rabbit anti-H3K4me1 (Abcam #8895)
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| Treatment protocol |
For RNA-Seq samples, CRC cells at ~0.5×10^6 cells/well in 6-well plates were treated with 500nM JQ1 for 0.5, 1, 6, or 24 hours, or 0 hours as a control
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| Growth protocol |
CRC cell lines were grown in MEM media supplemented as previously described, except for COLO205 cells which were grown in RPMI-1640 supplemented with 10% fetal bovine serum, 2 mM L-glutamine, and 1% penicillin/streptomycin.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-Seq, lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. For DNase Hypersensitivity, nuclei were isolated and treated with DNase I. For RNA-Seq samples, cells were lysed and RNA extracted with TRIzol according to the manufacturer’s protocol.
ChIP-Seq libraries were prepared with NEB reagents as previously described. Briefly, DNA was end-repaired and the blunt, phosphorylated ends were treated to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers and library fragments of ~250 bp were band isolated from an agarose gel. DNase Hypersensitivity libraries were prepared as previously described. Briefly, DNase I treated DNA was blunt-ended. DNA fragments were ligated to biotinylated linkers and digested with MmeI, producing 2 bp overhangs for ligation with a second linker or Illumina adapters. DNA was then PCR amplified and library fragments of ~86 bp were band isolated from a gel. RNA libraries were prepared for sequencing using standard Illumina protocols.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiScanSQ |
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| Data processing |
Adapter and quality trimming of both ChIP-Seq and RNA-Seq reads was done using FASTX Toolkit 0.0.13. Reads below 25bp in length or reads with Phred quality scores below 20 were discarded
ChIP-seq reads were aligned to hg19 with Bowtie2 version 2.0.6, using default parameters. RNA-Seq reads were aligned to hg19 using TopHat v1.3.2
Potential PCR duplicates were removed from aligned ChIP Seq reads files
ChIP-Seq peaks were called using MACS v1.4. Cufflinks v1.3.0, run with genomic bias correction, was used to calculate transcript abundancies in the RNA-Seq data.
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-Seq WIG tracks were generated with MACS v.14. The WIG signal was divided by mean WIG signal for each sample, and the WIGs were converted to bigWIGs
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| Submission date |
Feb 09, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter Scacheri |
| E-mail(s) |
pxs183@case.edu
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| Phone |
216-368-3458
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| Organization name |
Case Western Reserve University
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| Street address |
10900 Euclid Ave; BRB 647
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| City |
Cleveland Heights |
| State/province |
OH |
| ZIP/Postal code |
44106 |
| Country |
USA |
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| Platform ID |
GPL15456 |
| Series (1) |
| GSE77737 |
Hotspots of aberrant enhancer activity punctuate the colorectal cancer epigenome |
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| Relations |
| BioSample |
SAMN04482010 |
| SRA |
SRX1568649 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2058072_V389_H3K4me1.bw |
196.9 Mb |
(ftp)(http) |
BW |
| GSM2058072_V389_H3K4me1_peaks.bed.gz |
932.3 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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