Dataset Information

Quantitative Analysis of Wild Type and Neat1 -/- Cerebral Frontal Cortex Transcriptomes

ABSTRACT: Purpose: The goals of this study are to elucidate dowstream effects of lnc RNA, Neat1 deletion in cerebral frontal cortex of adult mice by comparing Next-generation sequencing -derived cortical transcriptome profiles (RNA-seq) between wild type and Neat1 knockout mice. Methods: Brain mRNA profiles of 2-4 moths-old wild-type (WT) and lnc RNA, Neat1 knockout (Neat1−/−) mice were generated by deep sequencing, using Illumina. Reads were mapped to mm10 reference genome using TopHat (version 2.0.9) and Bowtie (version 2.1.0), with the default parameters. Known iGenomes Ensembl mm10 were quantified by HTSeq (version 0.6.0) in intersection-strict mode. A sample-by-gene read count matrix was generated for all samples by the Ensembl genes. Scaling normalization to remove composition biases in sequencing data was applied to log(CPM) (read Counts Per Million total reads) using the trimmed mean of M-values (TMM) method. Results: RNA-seq showed near-complete depletion of Neat1 RNA levels. 1359 genes were differentially expressed in the frontal cortex of Neat1-/- mice. 25 of these differentially expressed genes withstood multiple testing corrections. Examination of RNA-seq data by principle component analysis showed two principle components that were mutually uncorrelated and orthogonal. Hierarchical cluster tree analysis showed that joined nodes from Neat1-/- samples were distanced from control subset cluster confirming the results of the PCA. Conclusions: Analyses of differentially expressed gene signature from NEAT1-/- mice revealed a significant impact on processes related to oligodendrocyte differentiation and RNA post-transcriptional modification with the underlying mechanisms involving Wnt signaling, cell contact interactions, and regulation of cholesterol/lipid metabolism.

ORGANISM(S): Mus musculus

PROVIDER: GSE126814 | GEO | 2019/02/21

REPOSITORIES: GEO

ACCESS DATA

Similar Datasets

Project description:Aim: We generated mice lacking Irs2 which mediates signaling pathways from insulin and IL-4 specifically in lyzM Cre expressing cells. We isolated BMDM from control and Irs2LyzM-/- mice and compared their differential gene expression under veihicle, IL-4 and LPS treatment by performing mRNA sequencing studies. Methods: BMDM from control and Irs2LyzM-/- mice were treated for 24 hours with vehicle, IL-4 (10 ng/ml) or LPS (100 ng/ml). RNA integrity was confirmed and concentration measured using a Bioanalyzer. cDNA libraries were created from up to 5 μg total RNA. There were three (Irs2LyzM-/-) and four (control) biological replicates for each group and each biological replicate was divided into eight technical replicates and sequenced on individual lanes on the Illumina HiSeq 2000 (100 bp paired-end read length) at the Sanger Institute. Raw reads from the sequenced RNAseq libraries were mapped with Tophat splice junction aligner (Kim, Pertea et al. 2013), version 2.0.8 against Ensembl mouse genome reference sequence assembly (mm9) and transcript annotations. All parameters were set to default except inner distance between mate pairs (r = 130). Gene-based read counts were then obtained using the HTSeq count module (version 0.5.4p3). Differential expression analysis was performed on the counts data using the DESeq2 Bioconductor package (version 1.16.1). The GSEA preranked tool from GSEA version 2.2.4 was used forGeneset enrichment analysis. Gene ontology enrichment analysis was also performed using the topGo Bioconductor package separately for up and down-regulated genes in the comparisons analysed ( A. Alexa, J. Rahnenfuhrer, topGO: Enrichment Analysis for Gene Ontology. R package version 2.24.0 (2016)). Results: The mRNA seq. results reveal an anti- inflammatory transcriptional profile in LPS-treated Irs2LyzM-/- BMDM compared to control BMDM. Deletion of Irs2 in BMDM under all conditions (vehicle, IL-4 and LPS) manifest alteratons in genes involved in scavenging catecholamines and supporting increased sympathetic innervation.

Dataset Information

Quantitative Analysis of Wild Type and Neat1 -/- Cerebral Frontal Cortex Transcriptomes

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure