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Series GSE196034 Query DataSets for GSE196034
Status Public on Jul 28, 2023
Title Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors [Hi-C]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Cohesin plays vital roles in chromatin folding and gene expression regulation, cooperating with such factors as cohesin loaders, unloaders, and the insulation factor CTCF. Although models of regulation have been proposed (e.g., loop extrusion), how cohesin and related factors collectively or individually regulate the hierarchical chromatin structure and gene expression remains unclear. We have depleted cohesin and related factors and then conducted a comprehensive evaluation of the resulting 3D genome, transcriptome and epigenome data. We observed substantial variation in depletion effects among factors at topologically associating domain (TAD) boundaries and on interTAD interactions, which were related to epigenomic status.
Overall design We used the in situ Hi-C protocol as described in Rao et al. (Rao et al., Cell, 2014, 10.1016/j.cell.2014.11.021). In brief, ~3 × 10^6 RPE cells were crosslinked with 1% formaldehyde for 10 min at room temperature, followed by an additional 5 min with 200 mM glycine in phosphate-buffered saline (PBS). Fixed cells were permeabilized in Hi-C lysis buffer (10 mM Tris-HCl, pH 8.0; 10 mM NaCl; 0.2% Igepal CA630; 1× protease inhibitor cocktail [Sigma]) on ice. The cells were treated with 100 U of MboI (New England Biolabs) for chromatin digestion, and the ends of digested fragments were labeled with biotinylated nucleotides followed by ligation. After DNA reverse crosslinking and purification, ligated DNA was sheared to a size of 300–500 bp using a Covaris S2 focused-ultrasonicator (settings: Duty Cycle, 10%; Intensity, 4; Cycles per Burst, 200; Duration, 55 sec). The ligated junctions were then pulled down with Dynabeads MyOne Streptavidin T1 beads (Thermo Fisher Scientific). The pulled-down DNA was end-repaired, ligated to sequencing adaptors, amplified on beads and purified using Nextera Mate Pair Sample Preparation Kit (Illumina) and Agencourt AMPure XP (Beckman Coulter). DNA was then sequenced to generate paired-end 150-bp reads using the Illumina HiSeq-2500 or X Ten system.
Web link
Contributor(s) Nakato R, Sakata T, Bando M, Shirahige K
Citation(s) 37726281
Submission date Feb 03, 2022
Last update date Oct 03, 2023
Contact name Ryuichiro Nakato
Phone +81-3-5841-1471
Organization name The University of Tokyo
Department Institute for Quantitative Biosciences
Lab Laboratory of Computational Genomics
Street address 1-1-1 Yayoi
City Bunkyo-ku
State/province Tokyo
ZIP/Postal code 113-0032
Country Japan
Platforms (1)
GPL20795 HiSeq X Ten (Homo sapiens)
Samples (31)
GSM5858314 Hi-C siCTCF replicate1
GSM5858315 Hi-C siCTCF replicate2
GSM5858316 Hi-C siCTCF 72h
This SubSeries is part of SuperSeries:
GSE196450 Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors
BioProject PRJNA803067
SRA SRP358053

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE196034_CTCFKD_merged.hic 3.7 Gb (ftp)(http) HIC
GSE196034_Control_merge_TAD.VC_SQRT.25000_blocks.bedpe.gz 240.0 Kb (ftp)(http) BEDPE
GSE196034_Control_merge_loop.VC_SQRT.merged_loops.bedpe.gz 1.4 Mb (ftp)(http) BEDPE
GSE196034_Control_merged.hic 4.3 Gb (ftp)(http) HIC
GSE196034_ESCO1KD_merged.hic 1.8 Gb (ftp)(http) HIC
GSE196034_NIPBLKD_merged.hic 4.5 Gb (ftp)(http) HIC
GSE196034_RAW.tar 47.7 Gb (http)(custom) TAR (of HIC)
GSE196034_Rad21KD_merged.hic 2.9 Gb (ftp)(http) HIC
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Raw data are available in SRA
Processed data provided as supplementary file

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