|
| Status |
Public on May 12, 2024 |
| Title |
K562 Hi-C rep1 |
| Sample type |
SRA |
| |
|
| Source name |
K562
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
|
| Growth protocol |
K562 cells were cultured using a medium consisting of Iscove’s Modified Dulbecco’s Medium (IMDM) + 10% Fetal Bovine Serum (FBS) + 1% non-essential amino acids + 1% pen/strep at 37 C with 5% of CO2. HEK293 cells were cultured using a medium consisting of Eagle’s Minimum Essential Medium (EMEM) + 10% Fetal Bovine Serum (FBS) + 1% pen/strep at 37 C with 5% of CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
We performed Hi-C on wild-type K562 cells with the Arima Hi-C kit (A510008) according to the manufacturer's protocols (3 replicates, 870 million reads total).
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The reads were then processed with the Juicer pipeline56 to generate HiC contact files for each replicate. We then used the peakHiC tool57 to call loops from each IR with the following parameters: window size = 80, alphaFDR = 0.5, minimum distance = 10kb, qWr = 1. Using these parameters each IR was looped to a median of 3 regions (range 0-7).
Assembly: hg38
Supplementary files format and content: Hi-C data is stored as contact map .hic format.
|
| |
|
| Submission date |
May 06, 2024 |
| Last update date |
May 12, 2024 |
| Contact name |
SIQI ZHAO |
| E-mail(s) |
szhao@wustl.edu
|
| Organization name |
Washington University in St. Louis
|
| Department |
Genetics
|
| Lab |
Cohen
|
| Street address |
Campus Box 8232 4515 McKinley Ave.
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63108 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE266730 |
Effect of genomic and cellular environments on gene expression noise |
|
| Relations |
| BioSample |
SAMN41239095 |
| SRA |
SRX24475833 |
