|
| Status |
Public on Mar 11, 2022 |
| Title |
Lamin AC KO cells, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
GM12878 cell line
|
| Organisms |
Homo sapiens; human gammaherpesvirus 4 |
| Characteristics |
cell line: GM12878
genotype: Lamin A/C KO
replicate: 2
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
5x10^6 cells per condition were collected for in situ Hi-C.
Libraries of total ligation products were produced using Ultralow Library Systems V2 (Tecan Genomics, part no. 0344NB-32) as per manufacturer’s protocol.
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
The GM12878 cell line is EBV positive.
Lamin AC KO cells, replicate 2
KO.2
|
| Data processing |
HiC data preprocessing done using HiC-Pro using EBV genome version NC_007605.1 with 1kb resolution.
Assembly: NC_007605.1
Supplementary files format and content: Processed data files contain the HiC-Pro output: count matrices (*_1000.matrix) and regions file (1000_abs.bed).
|
| |
|
| Submission date |
Mar 11, 2022 |
| Last update date |
Mar 26, 2022 |
| Contact name |
Priyankara J Wickramasinghe |
| E-mail(s) |
priyaw@wistar.org
|
| Phone |
2154956837
|
| Organization name |
The Wistar Institute
|
| Department |
Bioinformatics
|
| Lab |
Genomics
|
| Street address |
3601 Spruce Street
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL30446 |
| Series (2) |
| GSE198412 |
Nuclear lamina binds the EBV genome during latency and regulates viral gene expression [Hi-C] |
| GSE198413 |
Nuclear Lamina binds the EBV genome during latency and regulates viral gene expression |
|
| Relations |
| BioSample |
SAMN26580228 |
| SRA |
SRX14437360 |
