MicroRNA discovery in rabbit embryos and embryonic stem-like cells by SOLiD™ sequencing of small RNA libraries

In this study SOLiD™ deep sequencing technique was applied to discover rabbit specific miRNAs and obtain the miRNA expression profile in rabbit embryos and embryonic stem-like (ES-like) cells. We sequenced a small RNA library constructed with the SOLiD small RNA expression kit from total RNA of rabbit 6 and 7 days post-coitum (dpc) embryos and a Carnegie stage 17 embryo (14 dpc), germinal ridges containing primordial germ cells (PGCs) from 14 dpc embryos (mixed male and female) and rabbit embryonic fibroblast (rabEF) as a control. Massively parallel sequencing of amplified cDNA fragments using the SOLiD™ 3 System generated more than 14 million high-quality sequence reads. A total of 1693 expressing rabbit miRNAs (ocu-miRNAs) was identified based on comparison of the obtained sequence reads to the known human, mouse and bovine miRNA databases (miRBase). The high throughput sequencing approach allowed us to identify rabbit specific miRNAs, which have not yet been annotated, and enabled a semi-quantitative estimation of the relative expression level of ocu-miRNAs. The submitted data files obtained from SOLiD™ sequencing provide a resource for further studies of ocu-miRNAs in embryonic development and rabbit ES cell biology.