NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7669309 Query DataSets for GSM7669309
Status Public on Aug 02, 2023
Title SNU719 7.5uM DEC 72h b
Sample type SRA
 
Source name SNU719
Organism human gammaherpesvirus 4
Characteristics cell line: SNU719
cell type: Gastric Cancer
genotype: NA
treatment: 7.5uM DEC
time point: 72h
Extracted molecule genomic DNA
Extraction protocol 1 × 105 cells (>95% viability) were washed in 50 ml cold PBS, spun down at 500 x g and 4°C for 5min
Cells were resuspended in 50 ml cold ATAC-Resuspension Buffer (RSB) (10 mM Tris-HCl, pH7.4, 10 mM NaCl, 3 mM MgCl2) containing 0.1% IGEPAL CA-630, 0.1% Tween-20 and 0.01% Digitonin. Resuspended cells were kept on ice for 3 min, then washed with 1 ml cold ATAC-RSB containing 0.1% Tween-20 but no IGEPAL CA-630 or Digitonin. Pellet nuclei at 500 x g and 4°C for 10 min, and the supernatant was removed. The pellet was then resuspended in a 50 ml Tn5 transposase reaction mixture following the manufacturer’s protocol (Illumina Tagment DNA Enzyme and Buffer, Illumina) and incubated at 37°C for 30 min in a thermomixer with 300 rpm mixing. DNA was purified using a MinElute PCR purification kit (Qiagen) and eluted in 10 ml Elution Buffer for library amplification. PCR amplification of fragmented DNA was done using the NEBNext HiFi PCR mastermix (New England Bioloabs) with a universal forward and sample-specific reverse oligo for sample barcoding using the following PCR conditions: initial incubations of 72°C for 5 min and 98°C for 30 s, followed by 5 cycles of 98°C for 10 s, 63°C for 30 s, and 72°C for 1 min. Additional number of cycles was determined for each sample through a “side” qPCR reaction using an aliquot of the PCR as template to determine the number of cycles needed to reach 1/3 of the max fluorescence. PCR products were run on a 1% agarose gel, regions from ~50 bp to ~1 kb were excised, and DNA was extracted using a gel extraction kit (Qiagen).
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing ATAC-Seq raw reads were aligned using bowtie against the Human gammaherpesvirus 4 NC_007605.1, followed by HOMER to generate bigwig files
Assembly: Viral Genome Human gammaherpesvirus 4 NC_007605.1
Supplementary files format and content:ATAC-Seq raw reads were aligned using bowtie against the Human gammaherpesvirus 4 NC_007605.1, followed by HOMER to generate bigwig files
 
Submission date Jul 31, 2023
Last update date Aug 02, 2023
Contact name Priyankara J Wickramasinghe
E-mail(s) priyaw@wistar.org
Phone 2154956837
Organization name The Wistar Institute
Department Bioinformatics
Lab Genomics
Street address 3601 Spruce Street
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL33481
Series (2)
GSE239645 Decitabine disrupts EBV genomic epiallele DNA methylation patterns around CTCF binding sites to increase chromatin accessibility and lytic transcription in gastric cancer [ATAC]
GSE239770 Decitabine disrupts EBV genomic epiallele DNA methylation patterns around CTCF binding sites to increase chromatin accessibility and lytic transcription in gastric cancer
Relations
BioSample SAMN36772514
SRA SRX21198292

Supplementary file Size Download File type/resource
GSM7669309_SNU719_Aza_72h_rep_2.bw 68.9 Kb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap