|
Status |
Public on Apr 27, 2020 |
Title |
Control_WT_3 |
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: scrambled mimic (control) 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
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
Control 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
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|
|
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 |
SAMN11037861 |
SRA |
SRX5444440 |