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| Status |
Public on May 22, 2024 |
| Title |
Macaque_PFC_Hi-C |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Macaca mulatta |
| Characteristics |
genotype: Wild type
Sex: Male
age: 26 years post birth
tissue: Prefrontal cortex (PFC)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
0.2 g frozen PFC sample was ground in liquid nitrogen and prepared into cell suspension. The filtered cell suspensions were fixed in 1% formaldehyde for 30 min. The cross-linked DNA was digested with 200U MboI, and the digested fragment ends were filled with biotin-14-dATP, dCTP, dGTP and dTTP by DNA Polymerase I Klenow Fragment (NEB, #M0210L). The resulting blunt-end fragments were re-ligated by T4 DNA ligase. Then, the ligated cross-linked DNA was reversed by proteinase K. DNA purification was performed by removing biotin from unligated ends using T4 DNA polymerase. The resulting purified DNA was sheared to a length of 350~500 bp using Covaris M220 and biotin-labeled DNA was pulled down with Dynabeads M-280 Streptavidin (Invitrogen). The library preparation including end repair, adapter ligation and PCR amplification was performed using DNA library preparation kit (Vazyme, #ND607). The resulting libraries were sequenced by Illumina 150 bp paired-end sequencing.
Hi-C libraries were prepared using VAHTS Universal DNA Library Prep Kit for Illumina® V3 (Vazyme, #ND607) following manufacturer's instructions.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Hi-C of PFC of adult rhesus macaque
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| Data processing |
Basecalling was performed using Illunima Casava (version: 1.8).
We used HiC-Pro (version: 2.11.1) to perform preprocessing for Hi-C data of PFC of human and rhesus macaque. Paired-end reads in FASTQ file format were first aligned against the reference genome (GRCh38/hg38 for human and rheMac10Plus (40 gaps filling based on Mmul_10/rheMac10) for rhesus macaque) using Bowtie 2 (version: 2.3.5) with following parameters, global mapping: -very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder; local mapping: -very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder.
Stringent filtering processes were performed following HiC-Pro standard workflow to generate genome-wide valid contact pairs.
Cooltools (version: 0.8.8) was used to identify A/B compartments at 100 Kb resolution, with the genome divided into two distinct groups based on the sign of the first PC (PC1). The group with higher gene density was defined as compartment A, and the other was compartment B. TAD boundaries were detected using the insulation score method (Crane et al., 2015) at a resolution of 40 Kb. Consequently, TAD bodies were defined as genomic regions between two adjacent boundaries. Chromatin loops were called by HiCCUPS (version: 1.9.9) at 25 Kb resolution.
Assembly: Mmul_10 (40 gaps filling)
Supplementary files format and content: *.bed files refer to the genomic coordinates of 3D genome organizations, including A/B compartments, TADs and TAD boundaries.
Supplementary files format and content: *bedpe files refer to the genomic coordinates of chromatin loops.
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| Submission date |
Sep 19, 2022 |
| Last update date |
May 22, 2024 |
| Contact name |
Ying Liu |
| E-mail(s) |
ying.liu@pku.edu.cn
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| Organization name |
Peking University
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| Department |
College of Future Technology
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| Lab |
Laboratory of Mitochondrial and Metabolism Research
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| Street address |
5 Summer Palace Road, Haidian District, Beijing
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| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platform ID |
GPL27943 |
| Series (1) |
| GSE213693 |
Comparative 3D genomic architectures elucidate the function of the adaptive human-specific inversions in human brain evolution |
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| Relations |
| BioSample |
SAMN30927418 |
| SRA |
SRX17631524 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6592102_macaque_PFC_TADBoundary_bin40kb.bed.gz |
35.5 Kb |
(ftp)(http) |
BED |
| GSM6592102_macaque_PFC_TAD_bin40kb.bed.gz |
15.5 Kb |
(ftp)(http) |
BED |
| GSM6592102_macaque_PFC_compartment_bin100kb.bed.gz |
27.0 Kb |
(ftp)(http) |
BED |
| GSM6592102_macaque_PFC_loop_bin25kb.bedpe.gz |
6.9 Kb |
(ftp)(http) |
BEDPE |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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