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| Status |
Public on Dec 23, 2022 |
| Title |
GM12878_ChIATAC_5k_DD_B1T2 |
| Sample type |
SRA |
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| Source name |
GM12878
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| Organism |
Homo sapiens |
| Characteristics |
cell line: GM12878
cell numbers: 5,000
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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 |
ChIATAC libraries were performed by combining ChIAPET (Wang et al., 2021) and ATAC-seq protocol. Briefly, crosslinked cells are permeabilized, restriction enzyme digested, and ligated. Then the nuclei were subjected to in situ transposition, DNA were purified and amplified by PCR.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
ChIATAC
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| Data processing |
Library strategy: ChIATAC
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.
ChIATAC data 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). 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).
Genome_build: hg38
Supplementary_files_format_and_content: Intrachromosomal interaction with frequency at least 2 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 |
| Organization name |
The Jackson Laboratory
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| Department |
Genome Technologies
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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) |
| GSE194036 |
ChIATAC is an efficient strategy for multi-omics mapping of 3D epigenomes from low-cell inputs |
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| Relations |
| BioSample |
SAMN25125396 |
| SRA |
SRX13834306 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5825816_THG0024.hic |
93.9 Mb |
(ftp)(http) |
HIC |
| GSM5825816_THG0024_cisPET.itx.txt.gz |
16.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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