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Sample GSM3635618 Query DataSets for GSM3635618
Status Public on Apr 27, 2020
Title Control_N2A1
Sample type SRA
 
Source name Neuro-2a cells
Organism Mus musculus
Characteristics tissue: Brain
cell line: Neuro-2a
transfected with: control mimic
Treatment protocol Neuro-2a cells were transfected with 40 nM of a miR-138 or scrambled mimic for 24 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 Control transfected 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 human (hg19 build) or mouse (mm10 build) 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: hg19 (human), mm10 (mouse)
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 GPL19057
Series (2)
GSE127502 Identification of targets of miR-138 in Neuro-2a and 293T cells by RNAseq
GSE127504 Identification of herpes simplex virus 1 and host targets of miR-138 by combined RNAseq/PARCLIP
Relations
BioSample SAMN11037845
SRA SRX5444376

Supplementary file Size Download File type/resource
GSM3635618_Gmouse_counts.txt.gz 95.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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