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Sample GSM3635610 Query DataSets for GSM3635610
Status Public on Apr 27, 2020
Title miR-138_M138_2
Sample type SRA
Source name HSV-1 infected Neuro-2a cells
Organisms Mus musculus; Human alphaherpesvirus 1
Characteristics mouse cell line: Neuro-2a
transfected with: miR-138 mimic
virus genotype: M138 mutant
Treatment protocol Neuro-2a cells were transfected with 40 nM of a miR-138 or scrambled mimic for 24 h, and infected with WT or M138 virus (MOI = 10) for 16 h before performing RNAseq
Extracted molecule total RNA
Extraction protocol Total RNAs were purified using an RNeasyPlus Mini Kit following the manufacturer’s instructions (Qiagen)
mRNAs were isolated using a Takara mRNA Isolation Kit. Libraries were prepared using a PrepX RNA-seq Library Preparation Kit
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Description miR-138 transfected, infected with M138 virus
Data processing Reads were trimmed to remove adapters, low-quality reads, and reads less than 30 bases long using Trimmomatic (
The trimmed reads were aligned with the HSV-1 strain KOS (GenBank accession number KT899744.1) using Tophat2 (
Counts of reads aligned to each transcript were determined by Htseq-count (
Genome_build: Herpes simplex virus 1 strain KOS (GenBank accession number KT899744.1)
Supplementary_files_format_and_content: Tab-delimited text files containing raw counts of sequencing reads for each viral gene
Submission date Feb 28, 2019
Last update date Apr 28, 2020
Contact name Dongli Pan
Organization name Zhejiang University
Street address 866 Yuhangtang Road
City Hangzhou
State/province Zhejiang
ZIP/Postal code 110058
Country China
Platform ID GPL26237
Series (2)
GSE127501 Effects of host miR-138 on herpes simplex virus 1 gene expression in Neuro-2a cells and their dependence of the binding sites on ICP0 mRNA
GSE127504 Identification of herpes simplex virus 1 and host targets of miR-138 by combined RNAseq/PARCLIP
BioSample SAMN11037853
SRA SRX5444448

Supplementary file Size Download File type/resource
GSM3635610_KKOS_counts.txt.gz 507 b (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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