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Sample GSM3635603 Query DataSets for GSM3635603
Status Public on Apr 27, 2020
Title miR-138_WT_1
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: WT
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 WT virus
Data processing Reads were trimmed to remove adapters, low-quality reads, and reads less than 30 bases long using Trimmomatic (http://www.usadellab.org/cms/index.php?page=trimmomatic)
The trimmed reads were aligned with the HSV-1 strain KOS (GenBank accession number KT899744.1) using Tophat2 (https://ccb.jhu.edu/software/tophat/index.shtml).
Counts of reads aligned to each transcript were determined by Htseq-count (https://htseq.readthedocs.io/).
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
E-mail(s) pandongli@zju.edu.cn
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
Relations
BioSample SAMN11037860
SRA SRX5444441

Supplementary file Size Download File type/resource
GSM3635603_DKOS_counts.txt.gz 486 b (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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