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Sample GSM4319230 Query DataSets for GSM4319230
Status Public on Apr 27, 2020
Title N2AFox2
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 pFoxc1human transfected 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 SAMN14128576
SRA SRX7744829

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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