|
| Status |
Public on May 08, 2024 |
| Title |
siscramble rep2 |
| Sample type |
SRA |
| |
|
| Source name |
K562
|
| Organism |
Homo sapiens |
| Characteristics |
siqhic restriction_enzyme: Arima
cell line: K562
treatment: untreated
|
| Treatment protocol |
CTCF siRNA knockdown was performed using ON-TARGETplus SMARTpool Human CTCF (10664) siRNA (Dharmacon L-020165-00-0005). After 48 hr incubation, cells were harvested for Hi-C. Another Hi-C experiment was performed, where K562 cells were either treated with 0.1% DMSO or 10 uM etoposide for 72 hr.
|
| Growth protocol |
All the cells were cultured in RPMI-1640 supplemented with 10% Fetal Bovine Serum (FBS) and 1% penicillin-streptomycin. All cultures were maintained at 37 °C, 5% CO2 in a humidified incubator.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
One million siRNA-treated cells and four million of drug-treated K562 cells were individually fixed and subsequently mixed with fixed mouse 3T3 cells at a ratio of 4:1. The mixed cells were then used for Hi-C experiments using Arima-HiC kit (Arima Genomics) according to the manufacturer’s protocol.
Libraries were prepared using the KAPA Hyper-Prep Kit (KAPA), according to the Arima-HiC kit protocol.
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
These libraries are SIQHiC libraries, which encompass both human and mouse DNA.
The paired-end reads were mapped to merged hg19 and mm10 reference genome using BWA mem (0.7.17-r1188).
Subsequently, only the reads mapped to the human genome were retained for further analysis.
The mapped reads were then passed to Juicer pipeline (1.5.7) to perform chimeric reads analysis, merging, generating Hi-C matrix, loop calling using HiCCUPS, and TAD calling using Arrowhead.
Assembly: hg19
Supplementary files format and content: *_merged_nodups.txt.gz: tab-delimited text files include valid pairs for each Sample ...
Supplementary files format and content: *_30.hic: hic format files generated from Juicer and can be visualized by Juicebox
|
| |
|
| Submission date |
Jul 26, 2023 |
| Last update date |
May 08, 2024 |
| Contact name |
KAIJING CHEN |
| E-mail(s) |
KAIJING001@e.ntu.edu.sg
|
| Phone |
98667053
|
| Organization name |
Nanyang Technological University
|
| Department |
school of biological science
|
| Lab |
Melissa Fullwood
|
| Street address |
60 Nanyang Drive
|
| City |
Singapore |
| ZIP/Postal code |
637551 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE193413 |
Super-silencer perturbation by EZH2 and REST inhibition leads to large loss of chromatin interactions and reduction in cancer growth [Hi-C] |
| GSE193489 |
Super-silencer perturbation by EZH2 and REST inhibition leads to large loss of chromatin interactions and reduction in cancer growth |
|
| Relations |
| BioSample |
SAMN36715106 |
| SRA |
SRX21163577 |
