|
| Status |
Public on May 28, 2023 |
| Title |
YCCEL1 7.5uM DEC 2 |
| Sample type |
SRA |
| |
|
| Source name |
YCCEL1
|
| Organism |
human gammaherpesvirus 4 |
| Characteristics |
cell line: YCCEL1
cell type: Gastric Cancer
genotype: Decitibine 7.5uM
treatment: Day3
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted as follows using the DNeasy Blood & Tissue Kit (Qiagen, ID 69504) according to the manufacturer’s protocol.
genomic DNA was spiked with lambda phage DNA and digested with MspI restriction enzyme. Fragments were ligated with methylated adapters (NEB) to protect adapter sequences from downstream bisulfite treatment. Digested DNA was bisulfite converted using EZ DNA Methylation Kit (Zymo). All libraries were prepared using NEBNext adapters and indexed with i7 primers. These methylation- based libraries were spiked with 25% phiX Illumina library to ensure sequence diversity and sequenced 75bp paired-end on Illumina HiSeq 2500
Genomic DNA was bisulfite treated so that methylated cytosine residues were protected and unmethylated cytosines were converted to T in the final sequencing.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RRBS
|
| Data processing |
Adapter sequences were removed using TrimGalore
RRBS sequence alignment to the human gammaherpesvirus 4 (HHV4) NC_007605.1 was performed by Bismark
CpG counts were performed using bismark_methylation_extractor function and methylation coverage is provided as a processed file.
Assembly: Viral Genome Human gammaherpesvirus 4 NC_007605.1
Supplementary files format and content: bismark.cov.gz
|
| |
|
| Submission date |
May 24, 2023 |
| Last update date |
May 28, 2023 |
| Contact name |
Sarah Alp |
| E-mail(s) |
salp@wistar.org
|
| Organization name |
The Wistar Institute
|
| Street address |
3601 Spruce Street
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19401 |
| Country |
USA |
| |
|
| Platform ID |
GPL25190 |
| Series (2) |
| GSE233330 |
Decitabine disrupts EBV genomic epiallele DNA methylation patterns around CTCF binding sites to increase chromatin accessibility and lytic transcription in gastric cancer [RRBS] |
| GSE234658 |
Decitabine disrupts EBV genomic epiallele DNA methylation patterns around CTCF binding sites to increase chromatin accessibility and lytic transcription in gastric cancer |
|
| Relations |
| BioSample |
SAMN35348914 |
| SRA |
SRX20504959 |
