Despite being transcriptionally inactive and depleted of cytoplasm, sperm are known to contain diverse populations of both large (> 200 nt) and small (< 200 nt) RNA. Sperm-borne RNA have been implicated in male germ cell development, fertilization and early development, as well as the recently discovered phenomena known as ‘epigenetic transgenerational inheritance’ (ETI). Due to the unique characteristics of sperm RNA populations and the morphology of sperm themselves, isolating and analyzing sperm-borne RNA remains a challenge. For this reason, we established SpermBase to serve not only as a repository for sperm RNA expression data, but to also provide a standard approach to studying these peculiar RNAs. Our ‘modular’ standard approach to isolating sperm RNA is summarized on the Method page.

Currently, SpermBase contains large and small sperm-borne RNA expression data for mouse (M. musculus), rat (R. norvegicus), rabbit (O. cuniculus), and human (H. sapiens). In addition to whole sperm data, sperm head-only large RNA expression data is available for mouse, rabbit, and human; sperm head-only small RNA expression data is available for mouse and rabbit. Users may search for specific RNA species or types (e.g., miRNA, non-coding large RNA) on the Search page. All expression data on SpermBase is available for download; the sequencing data used for SpermBase may also be downloaded from GEO.

We will continue to add additional species in the future and submissions that conform to our standardized protocol are also welcome.

 

Schuster A, Tang C, Xie Y, Ortogero N, Yuan, S, Yan W (2016) SpermBase: a database for sperm RNA contents. Biology of Reproduction doi: 10.1095/ biolreprod.116.142190.

We recommand Anchor Alignment-Based Small RNA Annotation Pipeline (AASRA) for small RNA sequencing data analysis to get the most accurate results. If you use AASRA in your work, please cite one of the following: AASRA: An Anchor Alignment-Based Small RNA Annotation Pipeline Chong Tang, Yeming Xie, Wei Yan bioRxiv 132928; doi: https://doi.org/10.1101/132928