Read mapping metrics: For each single cell RNA sequencing sample the fraction of sequencing reads mapped to the human genome is shown and of those, the fraction of the reads that map to one unique genomic locus.
TECtool region classification: TECtool-inferred probabilities of each novel terminal exon being a terminal exon (Terminal), a cassette exon (Intermediate), or an intronic region (Background).

About

The terminal exons of human transcript isoforms contain 3' untranslated regions (3'UTRs). 3'UTRs harbor cis-regulatory elements, which play crucial roles in gene expression regulation by impacting transcript stability, translation and localization. However, a comprehensive analysis of 3' end sequencing data has revealed that large numbers of 3' end isoforms are not represented in current transcript model annotations (Gruber et al., 2016, Genome Research).

In a previous study we have shown that there exists an abundance of terminal exons that are expressed in subpopulations of single cells (Gruber et al., 2018, Nature Methods).
Following up this study we have collected, quality controlled and carefully curated 47 publicly available datasets that provide full-length transcript single cell RNA sequencing (scRNA-seq) data covering 61,692 single cell transcriptomes.

By applying our Terminal Exon Characterization tool, TECtool, separately to 53,069 high quality scRNA-seq libraries we have now screened these data to identify so far unknown terminal exons.

Our single cell-based Terminal Exon Annotation database (scTEA-db) provides the results of this annotation efforts. It enables to browse and filter 68,615 terminal exons identified from 101 cell types, 12,063 of which are unique and that are not yet part of the current gene annotation.

If you use any data obtained from scTEA-db, please cite: Miguel Barquin, Ian U. Kouzel, Beat Ehrmann, Michael Basler & Andreas J. Gruber. scTEA-db: a comprehensive database of novel terminal exon isoforms identified from human single cell transcriptomes, Nucleic Acids Research, 2024, https://doi.org/10.1093/nar/gkad878

Downloads

Full database (version 1.0, release date: 20230809) in tsv format: scTEA-db_v1.0
Description of database column names: scTEA-db_v1.0_columns_info
Gene annotation enriched by previously not annotated terminal exon 3' end isoforms (GTF format): GRCh38.102_scTEA_db_v1.0
Enriched terminal exon 3' end isoform annotation (GTF format): scTEA-db_v1.0

scTEA-db is developed by the GruberScienceLab. Data analysis and novel terminal exon discovery is done by Miguel Barquin. The scTEA-db Shiny web application* is developed and maintained by Ian Kouzel.
* performs best in Chrome, Firefox and Edge browsers

GitHub    Provide a feedback

© 2023 GruberScienceLab | University of Konstanz