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Sample GSM2267761 Query DataSets for GSM2267761
Status Public on Mar 01, 2017
Title Y881-920F_12.2
Sample type SRA
 
Source name Y881-920F infected MeWo cells; 12hpi
Organisms Homo sapiens; Human alphaherpesvirus 3
Characteristics cell line: MeWo
virus phenotype: Hyperfusogenic
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 SAMN05560341
SRA SRX2013148

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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