Mutants
Brn-3b knockout
SAMN37977830
External Id
University College London
INSDC center name
2024-05-01T00:53:50.737Z
INSDC first public
2024-05-01T00:53:50.737Z
INSDC last update
SRS19363620
INSDC secondary accession
live
INSDC status
Model organism or animal
NCBI submission model
Model.organism.animal.1.0
NCBI submission package
SRS19363620
SRA accession
2-4 months
age
C57BL
breed
2017/2022
collection_date
The aim of this study was to identify target genes regulated by the POU4F2 also called Brn 3b transcription factor in controlling vascular integrity and function. This was achieved using RNA sequencing to analyse for genes that were differentially regulated in the aorta of Brn 3b KO mouse mutants in which the Brn-3b gene was constitutively deleted when compared with aged matched littermate controls. For these studies, highly purified mRNA extracted from 3 Brn-3b KO aortas and wild-type littermate controls were used for RNA-dependent cDNA synthesis and first strand library preparation, prior to sequencing on the Illumina NextSeq 500 instrument (, San Diego, US) using paired end run. De-multiplexed data was converted to Fastq files using Illumina bcl2fastq Conversion Software v2.19, aligned with the reference genome using STAR (v2.5b), deduplicated using Picard Tools v2.7.1) and transcript reads were counted by FeatureCounts (v1.4.6p5). Ensembl ID for each gene was determined using gProfiler and this data was then used for normalisation, modelling and differential expression analysis using the iDEP.93 software platform, which connects multiple R/Bioconductor packages with annotation and pathway databases to provide comprehensive analysis of RNA sequencing data. Principal component analysis identified one outlier WT sample, which was taken into consideration in subsequent analyses as explained in the publication.
description
adult
dev_stage
United Kingdom
geo_loc_name
aorta
isolate
Mus musculus domesticus
http://purl.obolibrary.org/obo/NCBITaxon_10092
organism
male
sex
Brn-3b KO
strain
domesticus
sub_species
aorta
tissue
Model organism or animal sample from Mus musculus domesticus
title