RNA-sequencing reveals transcriptional signature of pathological remodeling in the diaphragm of rats after myocardial infarction

ABSTRACT: Purpose: In the current study, we used RNA-Seq to determine the transcriptional changes and understand the genetic reprogramming of the diaphragm in the chronic phase post-myocardial infarction. Methods: Rat diaphragm mRNA profiles 16 weeks post Sham and Myocardial infarction (MI) surgeries were generated by deep sequencing using llumina NextSeq 500. The sequence reads that passed quality filters were analyzed at the transcript level with TopHat followed by Cufflinks. Results: After quality control and data filtering, on average, 33,972,308 raw reads per sample were obtained. For each sample, 88.49 % to 91.70 % reads were uniquely mapped to the rat reference genome. Median CV coverage uniformity was 0.45± 0.01. Distribution of mapped reads over DNA regions showed 48% of reads mapped to coding region, 20% of reads mapped to untranslated region (UTR), 12% of reads mapped to intron region, and 20% reads mapped to intergenic region. The resulting Sham and MI transcriptomes, created from generated transcriptomes of each individual sample in each group and merged transcriptomes within the same group, were used for differential gene expression analysis. A total of 112 differentially expressed genes (DEGs) were identified out of a total of 9664 genes with measured expression in MI and Sham groups. Among DEGs, 42 were upregulated and 70 were downregulated in the MI group. Hierarchical clustering heat map, pathway enrichment and gene ontology (GO) analyses, and analysis of DEGs in the framework skeletal muscle-specific biological networks were performed. Conclusions: Our study represents the first detailed analysis of diaphragm transcriptomes post-myocardial infarction generated by RNA-Seq technology.

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE141859 | GEO | 2020/12/31

REPOSITORIES: GEO