|
| Status |
Public on Oct 11, 2023 |
| Title |
SNU719 DMSO rep1 |
| Sample type |
SRA |
| |
|
| Source name |
SNU719
|
| Organism |
human gammaherpesvirus 4 |
| Characteristics |
treatment: DMSO
cell line: SNU719
cell type: Gastric tubular adenocarcinoma
|
| Treatment protocol |
Treatment with PARP inhibitor Olaparib was given 72 h before collection at a concentration of 5 µM. 5 million cells per condition were collected for in-situ Hi-C as per Rao et al. Cell 2014.
|
| Growth protocol |
YCCEL1 and SNU719 cell lines were cultured in RPMI 1640 supplemented with Fetal Bovine Serum at a concentration of 10% and supplemented with 1% penicillin-streptomycin in a humidified incubator containing 5% CO2 at 37 ̊C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries of total ligation products were produced using Ultralow Library Systems V2 as per manufacturer’s protocol.
Purified libraries were then enriched for only EBV genome ligation products using myBaits enrichment kit as per manufacturer’s protocol.
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
S.D.1.n
|
| Data processing |
Illumina HiSeq 2500 paired-end sequencing
Sequenced reads were aligned to the EBV genome assembly (Genbank: NC_007605.1) using HiC-Pro v2.10.0 pipeline
DESeq2 was used to estimate significance of differential contact based on raw count matrix files.
Only significantly changed associations (FDR<5%) were kept
Interactions were plotted as circos graph using the circlize package (version 0.4.12) of R (version 4.0.5)
Assembly: NC_007605.1
Supplementary files format and content: Raw counts for each interactions
Supplementary files format and content: p- and q-value of interactions are provided in the matrix file
|
| |
|
| Submission date |
Aug 03, 2023 |
| Last update date |
Oct 11, 2023 |
| Contact name |
Italo Tempera |
| E-mail(s) |
itempera@wistar.org
|
| Organization name |
The Wistar Institute
|
| Street address |
3601 Spruce Street
|
| City |
Philadelphia |
| ZIP/Postal code |
10194 |
| Country |
USA |
| |
|
| Platform ID |
GPL25190 |
| Series (2) |
| GSE239989 |
The three-dimensional structure of the EBV genome plays a crucial role in regulating viral gene expression in EBVaGC [HiC] |
| GSE239995 |
The three-dimensional structure of the EBV genome plays a crucial role in regulating viral gene expression in EBVaGC |
|
| Relations |
| BioSample |
SAMN36826381 |
| SRA |
SRX21237131 |
