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| Status |
Public on Dec 23, 2022 |
| Title |
GM12878_CTCFChIAPET_B1T1 |
| Sample type |
SRA |
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| Source name |
GM12878
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| Organism |
Homo sapiens |
| Characteristics |
cell line: GM12878
cell numbers: 10,000,000
antibody: anti-CTCF antibody (Abcam, ab70303)
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| Growth protocol |
The GM12878 cells were cultured in RPMI 1640 (ThermoFisher; A10491), supplemented with 15% fetal bovine serum (ThermoFisher; 10082147). The cells were cultured at 37 °C, 5% CO2, and ambient oxygen levels as described by the Coriell Institute of Medical Research.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
In situ ChIA-PET libraries with antibody against RNAPII or CTCF were constructed using 10,000,000 FA-EGS-crosslinked cells from GM12878 cell cultures, following the in situ ChIA-PET protocol (Wang et al., 2021).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
CTCF ChIAPET
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| Data processing |
Library strategy: ChIAPET
ChIATAC and ChIA-PET data were processed using ChIA-PIPE pipeline (Lee et al., 2020) on hg38 reference genome. Interaction data or loops with significant (called with Chiasig method by Paulsen 2014; PMID: 25114054) PETs >= 3 and PET distance > 8 kb are used for downstream analyses. The peak intensity from MACS2 (Liu, 2014) output is normalized with “-SPMR” option (signal per million reads). Both ChIATAC and ChIA-PET data can be visualized on Juicebox as 2D contact maps by using Juicer software (Durand et al., 2016) version 1.6.2 to create .hic file format.
ChIA-PETdata was processed by ChIA-PET Utilities (CPU) (https://github.com/cheehongsg/CPU). CPU (options: stat -s -p -T 18 -t 16) removed the adaptors, and grouped the reads into three categories: PET reads, single tag reads and no-linker reads. Tags identified (>=16bp) and reads without linkers were mapped to hg38 using BWA alignment and mem according to the tag/read length. CPU further separated the mapping results into uniquely-mapped, multiply-mapped, and unmapped classes with the pairing consideration (options: pair -S -t 16) and removed duplicates generated by PCR amplification (dedup -g -t 16). Next, the non-redundant uniquely-mapped reads from 3 categories were merged and used for peak calling with MACS v2.1.1.20160309 (options: --keep-dup all --nomodel --extsize 250 -B --SPMR -g hs). CPU further clustered the non-redundant uniquely-mapped pair-end tags and grouped them as intra-chromosomal PET clusters (cis-interactions) and inter-chromosomal PET clusters (trans-interactions) (options: cluster -s 8000 -M -B 1000 -5 5, -20 -3 5, 480 -t 16 -O). The cis-interaction significance was assessed with ChiaSigScaled (https://github.com/cheehongsg/ChiaSigScaled ; options: -c 3 -t 16 -p -m 8000). Cis-interactions with member size >=3 and FDR < 0.05 were reported. The complete list trans interaction was reported here while additional filtering were applied (e.g. exclude singletons) for corresponding analyses in publication. (see details in publication).
Genome_build: hg38
Supplementary_files_format_and_content: Significant intrachromosomal interactions with frequency at least 3 PETs. Format: text file with 7-column (coordinates of 2 anchors at the first six columns, interaction frequency at the 7th).
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| Submission date |
Jan 19, 2022 |
| Last update date |
Dec 23, 2022 |
| Contact name |
Chia-Lin Wei |
| E-mail(s) |
weicl@uw.edu
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| Organization name |
University of Washington
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| Department |
The Northwest Genomics Center (NWGC)
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| Lab |
Genome Sciences
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| Street address |
3720 15th Ave NE
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195-5065 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE194036 |
ChIATAC is an efficient strategy for multi-omics mapping of 3D epigenomes from low-cell inputs |
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| Relations |
| BioSample |
SAMN25125401 |
| SRA |
SRX13834311 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5825821_GM12878_CTCFCHIAPET_peak_support_R1.itx.txt.gz |
978.5 Kb |
(ftp)(http) |
TXT |
| GSM5825821_LHG0052H.hic |
320.0 Mb |
(ftp)(http) |
HIC |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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