scAPAdb

scAPAdb provides a manually curated atlas of alternative polyadenylation (APA) events derived from single-cell RNA sequencing (scRNA-seq) to enable analysis of transcript diversification and gene expression regulation.

Key Features:

• Single-Cell Resolution: Compiles APA information at the single-cell level to capture cell-to-cell heterogeneity in APA usage.
• scRNA-seq Source: Entries are derived from scRNA-seq experiments rather than bulk 3'-seq or bulk RNA-seq, preserving single-cell APA profiles.
• Comprehensive Species Coverage: Includes data from over 360 scRNA-seq experiments spanning six species: Homo sapiens, Mus musculus, Oryza sativa L. (rice japonica and indica), Arabidopsis thaliana, Zea mays, and Chlamydomonas reinhardtii.
• Manual Curation: Manually curated annotations include poly(A) sites, APA events, and poly(A) signals to ensure data accuracy.

Scientific Applications:

• Gene Expression Regulation: Enables study of APA-mediated transcript diversification and its impact on gene expression regulation.
• Cellular Heterogeneity Studies: Supports analysis of heterogeneity in APA usage across cell types, tissues, and biological conditions.
• Disease Research: Facilitates investigation of APA dynamics in disease contexts to identify potential biomarkers or regulatory mechanisms.

Methodology:

Aggregates annotations from a large collection of scRNA-seq experiments and applies manual curation to identify and annotate poly(A) sites, APA events, and poly(A) signals.