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Sample GSM7679566 Query DataSets for GSM7679566
Status Public on Oct 11, 2023
Title SNU719 RNAseq rep1
Sample type SRA
Source name SNU719
Organisms Homo sapiens; human gammaherpesvirus 4
Characteristics genotype: WT
cell line: SNU719
cell type: Gastric tubular adenocarcinoma
infection: Human gammaherpesvirus 4
Growth protocol SNU719 cell line was 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 total RNA
Extraction protocol Total RNA from SNU719 cell line was isolated from 2x106 cells using a Direct-zol RNA Kit (Zymo Research, cat. No. R2050) according to the manufacturer’s protocol.
Libraries were prepared using the SENSE mRNA-Seq Library Prep Kit V2 (Lexogen) to generate Illumina-compatible sequencing libraries according to the manufacturer’s instructions
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description SNU.ctrl.1
Data processing RNA-seq data was aligned using bowtie2 against hg19 version of the Human genome.
All unaligned reads were then aligned against NC_007605.1 version of EBV genome
RSEM v1.2.12 software was used to estimate raw read counts and RPKM for Human and EBV genes
Assembly: hg19, NC_007605.1
Supplementary files format and content: Tab-delimited text file includes raw read counts for each replicate
Submission date Aug 03, 2023
Last update date Oct 11, 2023
Contact name Italo Tempera
Organization name The Wistar Institute
Street address 3601 Spruce Street
City Philadelphia
ZIP/Postal code 10194
Country USA
Platform ID GPL23185
Series (2)
GSE239994 The three-dimensional structure of the EBV genome plays a crucial role in regulating viral gene expression in EBVaGC [RNA-seq]
GSE239995 The three-dimensional structure of the EBV genome plays a crucial role in regulating viral gene expression in EBVaGC
BioSample SAMN36830413
SRA SRX21242651

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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