|
| Status |
Public on Oct 11, 2023 |
| Title |
YCCEL1 Input rep2 |
| Sample type |
SRA |
| |
|
| Source name |
YCCEL1
|
| Organism |
human gammaherpesvirus 4 |
| Characteristics |
chip antibody: none
cell line: YCCEL1
cell type: Gastric adenocarcinoma
|
| Treatment protocol |
25 milion cells per immunoprecipitation were collected and fixed with 1% formaldehyde for 15 min and then quenched with 0.25 M glycine for 5 min on ice. After 3 washes with 1X PBS, pellets were resuspended in 10 mL each of a series of two lysis buffers and resuspended in 1mL of the third lysis buffer before fragmentation in Covaris ME220 Ultrasonicator to generate chromatin fragments roughly 200–500 bp in size. Chromatin was centrifuged to clear debris and a 1:20 of this cleared chromatin was kept as standard input for comparison against immunoprecipitations. Chromatin was incubated rotating at 4° 1h with 25 µg H3K4me1 and 25 µg H3K27ac, then chromatin–antibody complexes were precipitated using 50 µL of Dynabeads Protein A incubated rotating at 4° overnight.
|
| 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 |
DNA was purified using Promega Wizard SV Gel and PCR Clean-up Kit
Libraries for sequencing were made using NEBNext Ultra II DNA Library Prep Kit
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| 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 BWA
Peak calling was performed using MACS2 with input DNA used as a reference set
deepTools 3.5.2 was used to generate bigWig files
UCSC Genome Browser was used for data visualization
Assembly: NC_007605.1
Supplementary files format and content: Coverage file in bigWig format
Supplementary files format and content: MACS2 narrowPeak output (except for Input samples)
|
| |
|
| 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) |
| GSE239987 |
The three-dimensional structure of the EBV genome plays a crucial role in regulating viral gene expression in EBVaGC [ChIP-seq] |
| GSE239995 |
The three-dimensional structure of the EBV genome plays a crucial role in regulating viral gene expression in EBVaGC |
|
| Relations |
| BioSample |
SAMN36826058 |
| SRA |
SRX21236963 |
