singleCellBase: a high-quality manually curated database of cell markers for single cell annotation across multiple species

Background: Annotating cells in the analysis of single-cell RNA-Seq (scRNA-seq) data is one of the most challenging tasks that researchers are actively addressing. Manual cell annotation is generally considered the gold standard method, although it is labor intensive and independent of prior knowledge. At present, the relationship between high-quality, known marker genes and cell types is very limited, especially for a variety of species other than humans and mice. Methods We manually reviewed thousands of published literatures, comprehensively curated the records on associations of cell type and gene markers. By organizing the records using MySQL based on relational schema, and constructing website based on Java Server Pages using the Java Servlet framework, we developed our singleCellBase database. Results The singleCellBase is a manually curated resource of high-quality cell types and gene markers associations across multiple species. In details, it offers 9,027 entries spanning a total of 2,610 cell types and linking with 21,044 genes (cell markers), covering 381 diseases/status, and 524 types of tissues across 33 species. The singleCellBase provides a user-friendly interface to the scientific community to browse, search, download and submit records of marker genes and cell types. Conclusions The resource providing ineluctable prior knowledge required by manual cell annotation, which is valuable to interpret scRNA-seq data and elucidate what cell type or cell state that a cell population represents.