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Sample GSM7425646 Query DataSets for GSM7425646
Status Public on May 28, 2023
Title SNU719 7.5uM DEC 2
Sample type SRA
 
Source name SNU719
Organism human gammaherpesvirus 4
Characteristics cell line: SNU719
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 SAMN35348910
SRA SRX20504963

Supplementary file Size Download File type/resource
GSM7425646_SNU_5aza2_CKDL210006321-1a-AK987-AK985_HFH77CCX2_L6_1_val_1_bismark_bt2_pe.bismark.cov.gz 171.8 Kb (ftp)(http) COV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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