|
| Status |
Public on Mar 01, 2017 |
| Title |
pOka-WT_12.2 |
| Sample type |
SRA |
| |
|
| Source name |
pOka infected MeWo cells; 12hpi
|
| Organisms |
Homo sapiens; Human alphaherpesvirus 3 |
| Characteristics |
cell line: MeWo
virus phenotype: Wild type
time post infection: 12
|
| Treatment protocol |
Infection with varicella-zoster virus
|
| Growth protocol |
MeWo cells were were propagated in culture medium [MEM supplemented with 10% fetal bovine serum (Life Technologies, Grand Island, NY), non-essential amino acids (100μM; Cellgro, Manassas, VA), penicillin-G/streptomycin (100 units/ml; Life Technologies, Grand Island, NY), amphotericin (0.5 mg/ml; Cellgro, Manassas, VA)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from melanoma cells using an RNeasy Plus Mini Kit (Qiagen)
Libraries were prepared from HOW MUCH RNA using a TruSeq RNA Preparation Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Quality control checks of FastQ files was performed using FastQC v0.11.4 Babraham Bioinformatics
Reads were aligned and BAM files generated using STAR v2.5
BAM files containing the aligned reads were used to generate RPKM values, which were calculated using the RNA-seq pipeline in Partek Genomics Suite 6.6
Genome_build: hg19
|
| |
|
| Submission date |
Aug 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Stefan Oliver |
| E-mail(s) |
sloliver@stanford.edu
|
| Organization name |
Stanford University School of Medicine
|
| Department |
Pediatrics
|
| Lab |
Arvin
|
| Street address |
300 Pasteur Drive, Grant Rm S366
|
| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL26132 |
| Series (1) |
| GSE85493 |
Cell responses to dysregulated VZV-induced cell-cell fusion |
|
| Relations |
| BioSample |
SAMN05560326 |
| SRA |
SRX2013145 |
