endo-siRBase: A multi-species developmental endo-siRNA repository and searchable database

Endogenous short interfering RNAs (endo-siRNAs) play an important role in gene regulation in many different model systems, yet to our knowledge there is no database that contains information for those that are experimentally validated. The endo-siRbase platform reported in this paper fills this void by housing endo-siRNA fasta files from several species. These files were generated from reads derived from small RNA datasets that did not map to miRNA, piRNA, or any other non-coding RNA but that did map antisense to annotated mRNA. This repository of endo-siRNAs is groundbreaking because it is the first to provide an official annotation while also citing the endo-siRNA experimental source and any available developmental information, such as stage or regional expression. In addition to providing validated endo-siRNA sequence information, endo-siRbase also provides a search tool that reports potential mRNA targets of an endo-siRNA sequence as well as any documented endo-siRNAs that are antisense to a specified mRNA. Due to the exponential growth of small RNA datasets and the mounting evidence for the critical role endo-siRNAs play in development, this database and search tool will benefit developmental biologists not only by providing an official annotation and a uniform identification procedure, but also by consolidating datasets into one location.