scPlantDB: a comprehensive database for exploring cell types and markers of plant cell atlases

Abstract

Abstract Recent advancements in single-cell RNA sequencing (scRNA-seq) technology have enabled the comprehensive profiling of gene expression patterns at the single-cell level, offering unprecedented insights into cellular diversity and heterogeneity within plant tissues. In this study, we present a systematic approach to construct a plant single-cell database, scPlantDB, which is publicly available at https://biobigdata.nju.edu.cn/scplantdb. We integrated single-cell transcriptomic profiles from 67 high-quality datasets across 17 plant species, comprising approximately 2.5 million cells. The data underwent rigorous collection, manual curation, strict quality control and standardized processing from public databases. scPlantDB offers interactive visualization of gene expression at the single-cell level, facilitating the exploration of both single-dataset and multiple-dataset analyses. It enables systematic comparison and functional annotation of markers across diverse cell types and species while providing tools to identify and compare cell types based on these markers. In summary, scPlantDB serves as a comprehensive database for investigating cell types and markers within plant cell atlases. It is a valuable resource for the plant research community.