|
| Status |
Public on Oct 11, 2023 |
| Title |
SNU719 H3K27ac HiChIP rep2 |
| Sample type |
SRA |
| |
|
| Source name |
SNU719
|
| Organisms |
Homo sapiens; human gammaherpesvirus 4 |
| Characteristics |
chip antibody: H3K27ac (Active Motif 39133)
cell line: SNU719
cell type: Gastric tubular adenocarcinoma
infection: Human gammaherpesvirus 4
|
| 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 |
25 million cells were fixed with 1% formaldehyde for 10 min and then quenched with 0.125 M glycine for 5 min at RT. Ligation products were immunoprecipitated with 25 µg H3K27ac (Active Motif 39133). 5 μL of Streptavidin C-1 beads were used for biotin pull-down.
After the last wash with Tween Wash Buffer bead-bound DNA was used to prepare libraries with Ultralow Library Systems V2 (Tecan Genomics, part no. 0344NB-32) as per manufacturer’s protocol
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| 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
hichipper software was used to perform restriction site bias modeling and interaction identification.
diffloop R package was used to estimate significance of differential contact based on raw count matrix files. Only significantly changed associations (FDR<1%) were kept
EBV-EBV interactions were visualized using UCSC Genome Browser, EBV-Human interactions were plotted as circos graph using the circlize package (version 0.4.12) of R (version 4.0.5)
Assembly: hg19, NC_007605.1
Supplementary files format and content: mango files listing all interactions with the respective p-value
Supplementary files format and content: bedpe files listing all interchromosomal interactions with respective read counts
Library strategy: HiChIP
|
| |
|
| 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 |
GPL23185 |
| Series (2) |
| GSE239992 |
The three-dimensional structure of the EBV genome plays a crucial role in regulating viral gene expression in EBVaGC [HiChIP] |
| GSE239995 |
The three-dimensional structure of the EBV genome plays a crucial role in regulating viral gene expression in EBVaGC |
|
| Relations |
| BioSample |
SAMN36830732 |
| SRA |
SRX21242816 |
