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Status |
Public on Dec 23, 2022 |
Title |
GM12878_CTCFChIAPET_B1T2 |
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 |
SAMN25125402 |
SRA |
SRX13834312 |
Supplementary file |
Size |
Download |
File type/resource |
GSM5825822_GM12878_CTCFCHIAPET_peak_support_R2.itx.txt.gz |
335.6 Kb |
(ftp)(http) |
TXT |
GSM5825822_LHG0066V.hic |
72.0 Mb |
(ftp)(http) |
HIC |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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