|
| 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 37ºC 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 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000409795.2/) and Human herpesvirus 1 strain KOS, complete genome (https://www.ncbi.nlm.nih.gov/nuccore/JQ673480.1)
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 |
| E-mail(s) |
garnham.a@wehi.edu.au
|
| 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 |
|
| Relations |
| BioSample |
SAMN07419216 |
| SRA |
SRX3042517 |
