Computational protocol: An integrated analysis revealed different microRNA mRNA profiles during skeletal muscle development between Landrace and Lantang pigs

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[…] RNA sequencing data obtained from the same tissues as those used in miRNA sequencing (Gene Expression Omnibus (GEO) under series GSE25406) were utilized. The reference genome index was built using the Bowtie2-build component of Bowtie2 (ver. 2.0) and SAMtools (ver. 0.1.18). Tophat2 (version 2.0.8) was applied to map the reads to the reference genome. The expression levels of each gene were normalized as FPKM (Reads per kilobase of exon model per million mapped reads) using the Refseq gene (mm10) model downloaded from the UCSC Browser gateway. Each FPKM was log2-transformed. [...] The biological process (BP) of each DE miRNA was annotated by the Blast2GO software ( GO functional classification and enrichment analysis were also conducted to identify GO terms that were significantly enriched in DE miRNAs using DAVID analysis ( Heatmaps were drawn for the DE miRNAs using the R language package “Pheatmap.” The myogenic DEGs and predicted gene interaction network was drawn using the STRING ( and Cytoscape 3.1.0 ( programs. The P-values were determined using T-tests. The statistical analyses were conducted with SPSS 10.0. […]

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