RATEmiRs: the rat atlas of tissue-specific and enriched miRNAs for discerning baseline expression exclusivity of candidate biomarkers

Abstract

MicroRNAs (miRNAs) are small RNAs that regulate mRNA expression and have been targeted as biomarkers of organ damage and disease. To explore the utility of miRNAs to assess injury to specific tissues, a tissue atlas of miRNA abundance was constructed. The Rat Atlas of Tissue-specific and Enriched miRNAs (RATEmiRs) catalogues miRNA sequencing data from 21 and 23 tissues in male and female Sprague-Dawley rats, respectively. RATEmiRs identifies tissue-enriched (TE), tissue-specific (TS), or organ-specific (OS) miRNAs via comparisons of one or more tissue or organ vs others. We provide a brief overview of RATEmiRs and present how to use it to detect miRNA expression abundance of candidate biomarkers as well as to compare the expression of miRNAs between rat and human. The database is

MicroRNAs as Biomarkers for Ionizing Radiation Injury

“…Some research reported the specific and enriched sites of miRNAs analyzed through the number of miRNAs present in various tissues and organs of rats and humans, which were detected via high-throughput sequencing. Bushel et al ( Bushel et al, 2020 ) constructed a tissue atlas of miRNA abundance with miRNAs sequencing data of tissues in rats. The atlas contains three bioinformatics pipelines to detect abundant miRNAs.…”

The Rapidly Evolving X-linkedmiR-506Family Finetunes Spermatogenesis to Enhance Sperm Competition

“…Several previous studies have shown that the X-linked miR-506 family miRNAs are predominantly expressed in the testis of multiple species (15,16,24,(37)(38)(39). By analyzing the publicly available small RNA sequencing (sRNA-seq) datasets from multiple species, including humans, rhesus monkeys, mice, rats, rabbits, dogs, and cows (27,40,41), we further confirmed that miR-506 family miRNAs were indeed highly abundant in the testis, but barely expressed in other organs (Fig. S6, and Table S3).…”