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Sample GSM5920578

Query DataSets for GSM5920578

Status

Public on Mar 01, 2022

Title

12w_CDS_4

Sample type

SRA

Source name

brain tissue

Organism

Mus musculus

Characteristics

strain: C57BL/6
treatment: CDS
tissue: medial prefrontal cortex
age: post natal day 84

Growth protocol

GSE168268

Extracted molecule

total RNA

Extraction protocol

The medial prefrontal cortex was removed from frozen brain specimens. Total RNA was isolated using the SPLIT RNA Extraction Kit (Lexogen), according to the manufacturer's instructions.
The TruSeq Stranded Total RNA Library prep kit (Illumina) with Ribosomal depletion, and dual barcoding (2x10 base pairs) was used to produce library constructs with an input of 400 ng total RNA.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

RNA Seq reads were mapped to mouse genome (GRCm38.p5) with STAR-version 2.7.3a (Dobin et al., 2013) using the default parameters.
Reads were assigned to genes with featureCounts (Liao et al., 2014) with folowing parameters: -t exon -g gene_id, gene annotation - Gencode GRCm38/vM12.
The differential expression analysis was carried out with DESeq2-version 1.22.1 (Love et al., 2014) using the deafult parameters. We kept genes that have at least 5 reads in at least 5 samples
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: XLSX file contains results of the differential expression analysis (Log2FC) and q-values

Submission date

Feb 28, 2022

Last update date

Mar 01, 2022

Contact name

Sina-Maria Schalbetter

E-mail(s)

sina.schalbetter@uzh.ch

Organization name

Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse

Street address

Winterthurerstrasse 260