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| Status |
Public on Sep 30, 2023 |
| Title |
HCT116-CTCF-ChIA-PET-Rep2 |
| Sample type |
SRA |
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| Source name |
HCT116
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
method: CTCF-ChIA-PET
antibody: CTCF (Abclonal, catalog# A1133)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The overall chromatin sample preparation for ChIA-PET is very similar to in situ Hi-C, except the proximity ligation step with biotin marked linkers and finally ligated chromatin enriched by interested protein factors (such as CTCF, cohesin, and RNAPII) in ChIA-PET.
Nextera DNA library prepration kit and corresponding protocol was used for the library prepation.
We applied Tn5 transponase in the Nextera DNA library preparation kit to cut chromatin DNA and paste the linker sequence to the DNA ends simutaneously. Then the ligated chromatin with biotin marked linkers will be enriched by streptavidin beads.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Sample 77
nuclear chromatin
CTCF-ChIA-PET
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| Data processing |
Library strategy: ChIA-PET
ChIA-PET fastq files were mapped by our ChIA-PET processing pipeline, available in github (ChIA-PIPE; Lee et al., 2020). 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. ChIA-PET loop files (bedpe) were generated by our ChIA-PET processing pipeline, available in github (ChIA-PIPE). 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 sample# 75, GM12878, and sample# 108, library ID: CHH0020 to produce peaks of samples# 76-93, HCT116). 2D contact map files (hic) were generated by Juicer Tools (Version 1.7.5) using chromatin interaction data.
Genome_build: hg38
Supplementary_files_format_and_content:
BE3: bedpe format, containing ChIA-PET loops (long-range interactions), filtered out low PET count score, collecting only bigger than or equal to PET count score 3. bedgraph: bedgraph format, containing a DNA-binding protein coverage. broadPeak: broadPeak format, containing peaks called by SPP software. hic: 2D contact map file using all chromatin interactions , visualized by Juicebox 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
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| 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 |
SAMN27064782 |
| SRA |
SRX14660853 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5983406_ChIA-PET_hg38_HCT116_CTCF_LHH0127V_novaseq_pairs.hic |
298.0 Mb |
(ftp)(http) |
HIC |
| GSM5983406_LHH0127V.e500.clusters.cis.BE3.txt.gz |
4.0 Mb |
(ftp)(http) |
TXT |
| GSM5983406_LHH0127V.for.BROWSER.sorted.bedgraph.gz |
1.0 Gb |
(ftp)(http) |
BEDGRAPH |
| GSM5983406_LHH0127V.no_input_all_peaks.narrowPeak.gz |
8.2 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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