|
| Status |
Public on Apr 27, 2020 |
| Title |
miR-138_M138_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: 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 (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 |
SAMN11037852 |
| SRA |
SRX5444449 |
