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Sample GSM5858344 Query DataSets for GSM5858344
Status Public on Jul 28, 2023
Title Hi-C siWAPL
Sample type SRA
 
Source name RPE cells
Organism Homo sapiens
Characteristics enzyme: MboI
treatment: WAPL siRNA
time point: 72h
Treatment protocol RNAi transfection was performed using Lipofectamine RNAiMAX (Thermo Fisher Scientific) in accordance with the manufacturer's protocol, using final RNA duplex concentration of 50 nM.
Growth protocol RPE cells were routinely cultured in DMEM supplemented with penicilline-streptomycin-L-glutamine solution (Wako) and 10% FBS.
Extracted molecule genomic DNA
Extraction protocol Hi-C experiments were performed using MboI restriction enzyme as previously described (Rao, S. S. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665-1680, doi:10.1016/j.cell.2014.11.021 (2014)). Briefly, RPE cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Cells were permeabilized and chromatin was digested with MboI restriction enzyme, and the ends of restriction fragments were labeled with biotinylated nucleotides and ligated. After crosslink reversal, DNA was purified and sheared with Covaris M220 (Covaris). Then point ligation junctions were pulled down with streptavidin beads.
Sequencing libraries were constructed using Nextera Mate Pair Sample Preparation Kit (Illumina) according to the manufacturer’s protocol with 15 PCR cycles.
 
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model HiSeq X Ten
 
Data processing Sequenced paired-end 150-bp reads were mapped to the human genome hg38 using Juicer version 1.5.7 (BWA 0.7.12-r1039) with default parameters.
Genome_build: UCSC hg38
Supplementary_files_format_and_content: The hic files were generated by juicertools version 1.9.9 with default parameters. We used "inter_30.hic" in which low-quality reads were filtered.
 
Submission date Feb 03, 2022
Last update date Jul 28, 2023
Contact name Ryuichiro Nakato
E-mail(s) rnakato@iqb.u-tokyo.ac.jp
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
 
Platform ID GPL20795
Series (2)
GSE196034 Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors [Hi-C]
GSE196450 Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors
Relations
BioSample SAMN25611539
SRA SRX14030468

Supplementary file Size Download File type/resource
GSM5858344_WAPLKD.hic 1.3 Gb (ftp)(http) HIC
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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