Profiling the retinal microRNA (miRNA) expression in rodents by Next-Generation Sequencing

Purpose: The study aimed to determine the expression profiles of retinal miRNA from adult Sprague Dawley (SD) rat and C57BL/6 mice. Methods: The profile of retinal miRNA transcriptom from rat (8 weeks old) and mice (8 weeks old) were generated by deep sequencing, in triplicate, using Illumina Hiseq-2500 RNA-seq platform. The sequence reads from all samples were analysed for overall quality, screened for the presence of any contaminants and trimmed accordingly. The cleaned sequence reads were then processed through the quantification modules miRDEEP2 ver2.0.0.7 pipeline for known miRNA expression profiling. Rat or mice miRNAs from miRBASE release21 were used for mapping and quantification. Results: We identified a total of 643 and 1294 miRNAs, that were expressed in the retina of rat and mouse, respectively. Moreover, with a readcount cutoff of >0.5, 475 and 614 miRNAs were identified in the retina of rat and mouse, respectively. Conclusion: Our study represents the first detailed analysis of retinal miRNA profile in adult rat and mouse. Our results also suggested that both species have a similar expression patterns of retinal miRNAs. The expression profiles of retinal miRNAs in the rat and mice were generated by deep sequencing, in triplicate, using an Illumina Hiseq-2500 RNA-seq platform.