Non-coding RNA profiling by high throughput sequencing
Summary
The rat has been used extensively as a model system for biological studies. However, its microRNA (miRNA) transcriptome has not been well established. Here, we constructed a comprehensive rat miRNA BodyMap based on miRNA-seq of 320 samples from 11 organs of both sexes of juvenile, adolescent, adult, and aged Fischer 344 rats. We quantified the expression profiles of 993 rat miRNAs, including 268 novel miRNA candidates. A large number of miRNAs showed organ-specific, age-dependent, or sex-specific expression patterns. Particularly, brain exhibited the strongest organ-enriched expression patterns, and testis showed the most strikingly age-dependent expression patterns. Interestingly, the expression levels of two clusters of miRNAs were highly correlated with those of mRNAs and were highly age dependent. The miRNA dataset along with previously reported mRNA data from the same set of samples represents a unique resource to improve understanding of rat transcriptome and subsequently better utilize rats for biomarker discovery.
Overall design
We constructed and sequenced miRNA-seq libraries from 320 total RNA samples derived from 16 female and 16 male rats of the Fischer 344 strain, including four rats for each sex under each of the four developmental stages, namely juvenile (2-weeks old), adolescence (6-weeks old), adult (21-weeks old), and aged (104-weeks old) and ten organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testis or uterus) per rat.
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