|
| Status |
Public on Apr 27, 2020 |
| Title |
N2AC3 |
| Sample type |
SRA |
| |
|
| Source name |
Neuro-2a cells
|
| Organisms |
Mus musculus; Human alphaherpesvirus 1 |
| Characteristics |
tissue: Brain
|
| Treatment protocol |
Neuro-2a cells in 24-well plates were transfected with 100 ng of plasmids for 40 hours, and then infected with KOS at an MOI of 1 for 5 hours, before being harvested by lysis buffer for RNA purification and RNAseq analysis.
|
| 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 |
BGISEQ-500 |
| |
|
| Description |
pcDNA transfected and KOS infected Neuro-2a cells
|
| 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 mouse (mm10 build) or HSV-1 strain KOS (GenBank accession number KT899744.1) genome 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: mm10 (mouse), HSV1 strain KOS (GenBank KT899744.1)
Supplementary_files_format_and_content: Tab-delimited text files containing raw counts of sequencing reads for each host gene
|
| |
|
| Submission date |
Feb 18, 2020 |
| Last update date |
Apr 27, 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 |
GPL28172 |
| Series (2) |
| GSE127504 |
Identification of herpes simplex virus 1 and host targets of miR-138 by combined RNAseq/PARCLIP |
| GSE145499 |
Identification of genes regulated by Foxc1, which is a host target of miR-138 |
|
| Relations |
| BioSample |
SAMN14128578 |
| SRA |
SRX7744827 |
