EXPERIMENT_TITLE: GSM6592101: Human_PFC_Hi-C; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: 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.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Structural variation (SV) is a class of genetic variants involving long stretches of DNA and provides substantial innovations for adaptation and evolution. Investigation of SV profiles and turnover in nonhuman primates can help answer fundamental questions, such as what makes us uniquely human. Here, we present the high-resolution comparative 3D genome organizations of prefrontal cortex (PFC) of adult human and rhesus macaque. Based on a comprehensive SV atlas in rhesus macaque populations, we found that inversions are selectively constrained from the perspective of 3D genome, those inducing dramatic changes in chromosomal conformation tends to be purged by the action of purifying selection, implying the inconspicuous adaptive roles of inversions associated with strong effects. Furthermore, by integrating comparative genomics and multi-omics data across human and rhesus macaque, such as gene structures, regulatory elements and 3D genomic organizations, we highlighted a category of human-specific inversions with strong effects and found that they had undergone rapid fixation and caused significant changes in gene expression in human brain development, which may represent a driving force in human brain evolution. Overall, our findings reveal the great value of comparative 3D Hi-C maps in elucidating the adaptive functions of structural variants. Overall design: Hi-C performed on prefrontal cortex (PFC) of an adult human and a rhesus macaque
SAMPLE_TITLE: Human_PFC_Hi-C
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Brain"}, {"TAG": "genotype", "VALUE": "Wild type"}, {"TAG": "Sex", "VALUE": "male"}, {"TAG": "age", "VALUE": "45 years old"}, {"TAG": "tissue", "VALUE": "Prefrontal cortex (PFC)"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: Human_PFC_Hi-C
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Human_PFC_Hi-C
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