title: RNA-Seq of Sus scrofa:blood
design: Libraries were constructed using the Illumina TruSeq Small RNA Sample Prep Kit and were sequenced on an Illumina HiSeq 2500 platform in a 50 bp, single-read sequencing run. Sequence quality was inspected with the FastQC program. Adapter sequences were trimmed using the fastx clipper program in FastX toolkits, resulting in miRNA sequences of ~22 nucleotides. Sus scrofa 2.10 genome assemblies were downloaded from ENSEMBL version 75, and the miRNA sequences were mapped to the genome using Novoalign. Reads mapped to individual miRNAs were counted using HTseq-count. Data normalization and differential expression analysis were conducted using the DESeq2 package. For clustering analysis, the log2 expression ratios of differentially expressed miRNAs between treated vs untreated (day 0) were computed. Hierarchical clustering using average linkage and uncentered correlation was carried out using Cluster 3.0. The result was visualized using TreeView.