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Sample GSM2719510 Query DataSets for GSM2719510
Status Public on Feb 13, 2018
Title HSV-1 infected (negative) vero cells replicate 2
Sample type SRA
Source name Vero cells
Organisms Chlorocebus aethiops; Human alphaherpesvirus 1
Characteristics infection: Herpes simplex virus 1
infection status: Negative
cell line: Vero cells
Treatment protocol 1x10^6 Vero cells were infected with 0.5 MOI HSV-1-mCherry for 48 hours and HSV-1+ and HSV-1- cells were sorted based on mCherry fluorescence. Uninfected cells were used as a negative control. Three independent biological replicates of each condition were obtained via FACS sorting on an BD FACSAria III or BD FACSAria Fusion
Growth protocol Vero cells were grown in DMEM supplemented with 10% FCS at 37ÂșC 5% CO2
Extracted molecule total RNA
Extraction protocol RNA was extracted using the RNeasy Plus mini kit (QIAGEN) followed by concentration quantification and quality control using TapeStation 2200 (Agilent Technologies).
RNA sequencing libraries were prepared using the Illumina TruSeq stranded total RNA library prep kit and sequenced on an Illumina NextSeq 500. On average, 45.4 million 75 base pair paired-end reads were obtained for each sample.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Data processing FASTQ files were output using standard Illumina protocols and software.
Reads were aligned to the green monkey and HSV1 genomes simultaneously by Rsubread version 1.22.2
Read counts were summarized by Entrez Gene ID and gene locus tag ID for the green monkey and HSV1 genomes respectively
Genome_build: Chlorocebus_sabeus 1.1 ( and Human herpesvirus 1 strain KOS, complete genome (
Supplementary_files_format_and_content: Tab-delimited text files were written from the R promp. Columns represent Gene ID (Entrez ID for green monkey files and locus tag for HSV1 files), total gene length (total base count of all exons) and the number of reads mapping to that gene
Submission date Jul 27, 2017
Last update date May 15, 2019
Contact name Alexandra Garnham
Organization name Walter and Eliza Hall Institute of Medical Research
Street address 1G Royal Parade
City Parkville
State/province Victoria
ZIP/Postal code 3052
Country Australia
Platform ID GPL23837
Series (1)
GSE101960 Detection of viral double-stranded RNA from Vero cells infected with HSV-1-mCherry
BioSample SAMN07419216
SRA SRX3042517

Supplementary file Size Download File type/resource
GSM2719510_HSV1neg2_GreenMonkey_GeneCounts.txt.gz 132.2 Kb (ftp)(http) TXT
GSM2719510_HSV1neg2_HSV1_GeneCounts.txt.gz 601 b (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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