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| Status |
Public on Sep 30, 2023 |
| Title |
HCT116-RAD-mAC-auxin-9h-CTCF-ChIP-seq-Rep1 |
| Sample type |
SRA |
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| Source name |
HCT116-RAD-mAC-auxin
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116-RAD-mAC
treatment: auxin-9h
method: CTCF-ChIP-seq
antibody: CTCF (Abclonal, catalog# A1133)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The fixed cells were lysed. The chromatin was sonicated to generate DNA fragments averaging 200-500 bp in length .
We followed the protocol in the KAPA HyperPrep kit for the library preparation.
The adaptors were ligated at the two ends of DNA fragments. The DNA fragments with adaptors will be amplified.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Sample 102
nuclear chromatin
CTCF-ChIP-seq
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| Data processing |
ChIP-seq fastq files were mapped by BWA (version 0.7.7) with mem command. DNA-binding protein coverage files (bedgraph) were generated by bedtools (version 2.26.0) with genomecov command. Coverage files were sorted by chromosome and coordinate. Peaks (broadPeak, bed file type) were called by SPP (version 1.13) with our input control file, (sample# 63, library ID: CHG0033 to produce peaks of samples# 94 and 95, GM12878, and sample# 108, library ID: CHH0020 to produce peaks of samples# 96 - 107, HCT116).
Genome_build: hg38
Supplementary_files_format_and_content:
bedgraph: bedgraph format, containing a DNA-binding protein coverage. broadPeak: broadPeak format, containing peaks called by SPP software.
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| Submission date |
Mar 29, 2022 |
| Last update date |
Sep 30, 2023 |
| Contact name |
Yijun Ruan |
| E-mail(s) |
yijun.ruan@jax.org
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| Organization name |
The Jackson Laboratory
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| Department |
Ruan
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| Lab |
Ruan
|
| Street address |
10 DISCOVERY DR
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| City |
FARMINGTON |
| State/province |
CT |
| ZIP/Postal code |
06032 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE158897 |
Cohesin-mediated chromatin folding dynamics and transcriptional interactions |
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| Relations |
| BioSample |
SAMN27064757 |
| SRA |
SRX14660878 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5983431_CHH0062.q30.nr.sorted.bedgraph.gz |
746.8 Mb |
(ftp)(http) |
BEDGRAPH |
| GSM5983431_CHH0062.q30.sorted.nr.spp.z6.broadPeak.gz |
677.7 Kb |
(ftp)(http) |
BROADPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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