Alternative polyadenylation (APA) has been widely recognized as an important mechanism
in posttranscriptional regulation.
Increasing studies have revealed the role of APA in several biological processes, such as cell differentiation, stress responses and proliferation.
APA often occurs in a tissue-specific manner as documented in previous studies.
Furthermore, recent studies have detailed the existence of cell-type-specific APA preference
within the same tissue. Thus, exploration of APA at cell-type level could expand our understanding of APA, such as in cell identity determination.
To leverage the wealth of accumulated scRNA-seq, we collected and processed
about 150TB 10X Genomics scRNA-seq data from 24 human and 25 mouse normal tissues,
including 299 human cell types and 286 mouse cell types.
We utilized the scAPA method to identify polyA sites and quantitatively infer APA at cell-type level.
Thus, we could profile the APA landscape and identify cell-type-specific APA events for each cell type
in a certain tissue.
We also examined the correlations between APA and the corresponding gene expression level
to explore the effects of polyA site choice on gene expression.
In addition, the potential binding information of microRNAs (miRNAs) and RNA-binding proteins (RBPs)
on alternative regions regulated by cell-type-specific APA events has been estimated.
Integrating all these results, scAPAatlas is a comprehensive resource designed for users to
explore APA at cell-type level and elucidate biological functions of APA.
In scAPAatlas, users can:
Get a glimpse of the taxonomy of cell types in different tissues
Explore the APA landscape of different cell types within tissue or across tissues
Browse, search or visualize cell-type-specific APA events in different tissues
Browse, search or visualize APA events correlated with gene expression level
Browse, search or visualize miRNA-binding sites to explore crosstalk between miRNA and APA events
Browse, search or visualize RBP-binding sites to explore crosstalk between RBP and APA events
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