Expression Atlas

RNA-Seq Pipeline

The raw RNA-Seq reads were pre-processed to remove adapters and low quality bases using Trimmomatic (v0.36). The high-quality reads were aligned to the corresponding reference genome using STAR (v2.5.1), then unmapped reads were extracted for further mapping by HISAT2 (v2.0.3-beta) to improve reads utilization. The Picard tool (v2.1.1) was used to merge the two bam files. We computed Fragments Per Kilobase per Million mapped reads (FPKM) values for each gene by StringTie (v1.3.4). And tissue specificity index, tau, was newly added using in-house Perl scripts. We provide download of expression matrix files for eight ruminant species, which can facilitate screening genes of interest according to the tau value and tissue expression level.

RNA-Seq Collections

The expression atlas includes 1,936 RNA-seq datasets (goat: 300, sheep: 832, cattle: 461, zebu: 128, yak: 88, water buffalo: 69, roe deer: 20, and sika deer: 38). Click on the related species to search gene expression in heatmap and Genome Browser.