Functional Annotation of the Transcriptome of the Pig, <i>Sus scrofa</i>, Based Upon Network Analysis of an RNAseq Transcriptional Atlas.

ABSTRACT: The domestic pig (Sus scrofa) is both an economically important livestock species and a model for biomedical research. Two highly contiguous pig reference genomes have recently been released. To support functional annotation of the pig genomes and comparative analysis with large human transcriptomic data sets, we aimed to create a pig gene expression atlas. To achieve this objective, we extended a previous approach developed for the chicken. We downloaded RNAseq data sets from public repositories, down-sampled to a common depth, and quantified expression against a reference transcriptome using the mRNA quantitation tool, Kallisto. We then used the network analysis tool Graphia to identify clusters of transcripts that were coexpressed across the merged data set. Consistent with the p

SUBMITTER: Summers KM 

PROVIDER: S-EPMC7034361 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature