GSE193608
Comparative Transcriptomic Profiles of Adipocyte in Differentiation Process Provide Insights into Different Mechanisms of Adipogenesis between Subcutaneous and Intramuscular Fat Tissues in Pig [miRNA-seq]
Purpose: In this study, RNA-Seq was performed on intramuscular adipocytes and subcutaneous adipocytes at 0, 2, 4, and 8 days of differentiation to find genes and miRNAs that regulate the differentiation of two types of adipocytes. Method:The clean reads were mapped to the pig reference genome (scrofa. Sscrofa11.1) with perfect matches using Bowtie software. Annotated tRNA, rRNA, snoRNA, and snRNA sequences were filtered out, and conserved miRNAs were identified by the BLAST method against miRBase. The miRDeep2 software was used to predict new miRNAs based on the characteristics of the miRNA precursor hairpin structure. Differential expression analysis of two groups was performed using the DESeq2 R package. Differentially expressed miRNAs (DE-miRNAs) were screened with criterion of fold change?>?1.5 and FDR < 0.05 using DESeq2. Target genes of DE-miRNAs were predicted by miRanda and targetscan. Results: We found 30 genes that mainly regulate the differentiation of subcutaneous adipocytes and 22 genes that mainly regulate the differentiation of subcutaneous intramuscular adipocytes. A total of 17 important candidate differential miRNAs were found, of which 4 miRNAs are believed to play a regulatory role in both types of cells, and 10 and 3 act on lipid deposition in subcutaneous and intramuscular adipocytes, respectively. Overall design: RNA-Seq was performed on intramuscular adipocytes and subcutaneous adipocytes at 0, 2, 4, and 8 days of differentiation to find genes and miRNAs that regulate the differentiation of two types of adipocytes.