|
Status |
Public on Mar 11, 2022 |
Title |
Lamin AC WT cells, replicate 1 |
Sample type |
SRA |
|
|
Source name |
GM12878 cell line
|
Organisms |
Homo sapiens; human gammaherpesvirus 4 |
Characteristics |
cell line: GM12878 genotype: Lamin A/C WT replicate: 1
|
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 WT cells, replicate 1 WT.1
|
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 |
SAMN26580231 |
SRA |
SRX14437357 |