ScAPAdb: a comprehensive database of alternative polyadenylation at single-cell resolution. Issue Volume 50:Issue D1(2022) (11th September 2021)

• Record Type: Journal Article
• Authors: Zhu, Sheng; Lian, Qiwei; Ye, Wenbin; Qin, Wei; Wu, Zhe; Ji, Guoli; Wu, Xiaohui
• Is Part Of: Nucleic acids research. Volume 50:Issue D1(2022)
• Page Start: D365
• Page End: D370
• Publication Date: 2021-09-11
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkab795
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract: Alternative polyadenylation (APA) is a widespread regulatory mechanism of transcript diversification in eukaryotes, which is increasingly recognized as an important layer for eukaryotic gene expression. Recent studies based on single-cell RNA-seq (scRNA-seq) have revealed cell-to-cell heterogeneity in APA usage and APA dynamics across different cell types in various tissues, biological processes and diseases. However, currently available APA databases were all collected from bulk 3′-seq and/or RNA-seq data, and no existing database has provided APA information at single-cell resolution. Here, we present a user-friendly database called scAPAdb (http://www.bmibig.cn/scAPAdb ), which provides a comprehensive and manually curated atlas of poly(A) sites, APA events and poly(A) signals at the single-cell level. Currently, scAPAdb collects APA information from > 360 scRNA-seq experiments, covering six species including human, mouse and several other plant species. scAPAdb also provides batch download of data, and users can query the database through a variety of keywords such as gene identifier, gene function and accession number. scAPAdb would be a valuable and extendable resource for the study of cell-to-cell heterogeneity in APA isoform usages and APA-mediated gene regulation at the single-cell level under diverse cell types, tissues and species.