|
Status |
Public on Oct 11, 2023 |
Title |
SNU719 RNAseq rep2 |
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.2
|
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 |
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 |
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 |
|
Relations |
BioSample |
SAMN36830412 |
SRA |
SRX21242652 |