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Sample GSM5133352 Query DataSets for GSM5133352
Status Public on Jan 17, 2022
Title E1_rep2
Sample type SRA
 
Source name Prefrontal cortex
Organism Mus musculus
Characteristics tissue: Prefrontal cortex
strain: BALB/c
treatment: water
behavior: Control
Extracted molecule total RNA
Extraction protocol Prefrontal cortex tissues were removed, flash frozen on dry ice, and RNA was extracted using Direct-zol RNA kit. SureSelect Strand-Specific RNA Library Prep for Illumina (Agilent Technology) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Data processing Sequencing adaptors, low quality reads, and bases were trimmed with Trimmomatic-0.32 tool.
The sequence reads were aligned to the mouse reference genome (mm10) using Tophat 2.0.13 (bowtie2-2.2.3), which can adequately align reads onto the location including splice sites in the genome sequence.
The aligned reads were subjected to downstream analyses using StrandNGS 2.6 software (Agilent Technologies). The read counts allocated for each gene and transcript (UCSC version 2013.3.6) were quantified using a Trimmed Mean of M-value (TMM) method.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for every gene and every sample (all data are summarized in single file)
 
Submission date Mar 03, 2021
Last update date Jan 17, 2022
Contact name Shusaku Uchida
E-mail(s) uchida.shusaku.3n@kyoto-u.ac.jp
Organization name Kyoto University
Street address 53 Kawaharamachi, Sakyo-ku
City Kyoto
State/province Kyoto
ZIP/Postal code 606-8507
Country Japan
 
Platform ID GPL18480
Series (1)
GSE168172 RNA sequencing analysis of gene expression in the prefrontal cortex of mice treated with antidepressant drugs
Relations
BioSample SAMN18128675
SRA SRX10229621

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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