Conjoint analysis of RNA-seq and Solexa sequencing data of bovine mammary epithelial cells isolated from Chinese Holstein cows with high and low milk fat percentages

For RNA-seq, the sequencing library of each RNA sample was prepared by using Ion Total RNA-Seq Kit v2. For Solexa suquencing, we download the data obtained by a previous study in our laboratory. Genes and miRNAs were considered differentially expressed according to log2FC >1 or log2FC <-1and FDR <0.05. All target genes regulated by DERs were predicted by the combination of miRbase (http://www.mirbase.org) and TargetScan (http://www.targetscan.org). All the predicted target genes were intersected with the DEGs obtained by RNA-seq, and then the DEGs and DERs were obtained by a combined analysis.In total, 190 DEGs were regulated by 33 DERs that were significantly enriched in 488 GO terms and 12 KEGG pathways (p <0.05).This is of great significance for research on miRNAs and functional genes for the milk fat percentage- and marker-assisted selection of dairy cattle. two bovine mammary epithelial cells isolated from Chinese Holstein cows with high (4.85%) and low (3.41%) milk fat percentages