scTHREAD: a cell-resolved long-read transcriptome database with linked isoform, poly(A), junction, and allelic evidence

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ID: 333605
2026
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Abstract
Abstract Cell-resolved transcript structures are essential for understanding how isoform usage, alternative polyadenylation, and allelic expression vary across cell types. However, existing single-cell long-read datasets remain fragmented across studies, platforms, species, and workflows, hindering comparison and reuse. Here, we present scTHREAD (single-cell Transcriptome Hub for Long-Read Evidence, Annotation, and Discovery; https://scthread.ai4sc.ac.cn/), an open-access database for integrating, exploring, and retrieving single-cell long-read transcriptomic evidence. It comprises 453 runs from 34 human and mouse datasets, covering 923 389 cells profiled by Oxford Nanopore and PacBio. A uniform, platform-aware workflow catalogues 12 471 531 run–transcript observations, of which 30% carry one of 210 341 distinct Ensembl transcript identifiers. Isoform and poly(A)-site usage, splice-junction support, and allele-aware counts remain linked to their source study, run, cell type, and single cell, ensuring full provenance, and differential usage is precomputed where coverage permits. Records are explored through a web interface and retrieved through bulk downloads or a documented API. scTHREAD recapitulates known cell-type-specific isoform patterns and identifies reproducible monocyte–T-cell differences in CCND3, CUTA, and PSMB8 junction usage across three cohorts and two sequencing technologies, establishing it as a traceable resource for investigating RNA processing and transcript regulation at isoform resolution.
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openalex_W7223357521 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Zhi-Can Fu, Yelian Yan, Chunchun Wu, Ran Song, Xiaobo Wang, Jianfan Wei, Zhuangzhuang Lu, Tietuo Tao, Peng Lü, Wentao Cui, Yanqiang Li, Keyi Wu, Yong Chen, Tao Huang, Shenli Yuan
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Journal Nucleic Acids Research
Year 2026
DOI
10.1093/nar/gkag1038
URL
https://doi.org/10.1093/nar/gkag1038
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