|
| Status |
Public on May 08, 2024 |
| Title |
combined 24H rep2 |
| Sample type |
SRA |
| |
|
| Source name |
K562 cells with combination of GSK343 and X5050 for 24h
|
| Organism |
Homo sapiens |
| Characteristics |
hic restriction enzyme: Arima
treatment: treated with GSK343 and X5050 for 24 hours
cell line: K562
|
| Treatment protocol |
EV, S1KO, S2KO and DKO cells undergoes the CRISPR excision. The drug treated K562 cells were either treated with DMSO-72h, 5uM GSK343-72h, 100uM X5050-72h or combinational treatment (5uM GSK343+100uM X5050-72h). The time course GR treatment was done for either 8h or 24h treatment of the same concentration of GR as 72h.
|
| 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 cells was fixed and used for HiC experiment 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 |
| |
|
| Description |
24H_combined_merged_nodups.txt.gz
24H_combined_inter_30.hic
|
| Data processing |
The two replicates were combined and paired-end reads are mapped separated using BWA mem (0.7.17-r1188) to hg19 reference genome. The mapped reads are 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.
Genome_build: 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 |
Jan 10, 2022 |
| 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 |
SAMN24836410 |
| SRA |
SRX13718878 |
