|
| Status |
Public on Jul 28, 2023 |
| Title |
Hi-C siCTCF 72h |
| Sample type |
SRA |
| |
|
| Source name |
RPE cells
|
| Organism |
Homo sapiens |
| Characteristics |
enzyme: MboI
treatment: CTCF siRNA#1
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 |
SAMN25611514 |
| SRA |
SRX14030440 |
