|
| 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 |
| 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 |
SAMN36830413 |
| SRA |
SRX21242651 |
