scTHREAD: a cell-resolved long-read transcriptome database with linked isoform, poly(A), junction, and allelic evidence
6 affiliations
- 1Beijing Life Science Academy, Key Laboratory of Biosynthesis and Biomanufacturing in Model Plants, Ministry of Industry and Information Technology, and GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University , Guangzhou 511436 ,
- 2Zhongshan Hospital, Fudan University , Shanghai 200032 ,
- 3State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive Medicine, Institute of Women, Children and Reproductive Health, Shandong University , Jinan 250012 ,
- 4Guangzhou National Laboratory, The Guangdong-Hong Kong-Macao Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University , Guangzhou 511436 ,
- 5Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University , Beijing 100193 ,
- 6Department of Urology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an Jiaotong University , Xi’an 710061 ,
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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BibTeX
@article{fu2026scthread,
title = {{scTHREAD: a cell-resolved long-read transcriptome database with linked isoform, poly(A), junction, and allelic evidence}},
author = {Zhi-Can Fu and Yelian Yan and Chunchun Wu and Ran Song and Xiaobo Wang and Jianfan Wei and Zhuangzhuang Lu and Tietuo Tao and Peng Lu and Wentao Cui and Yanqiang Li and Keliang Wu and Yong Chen and Tao Huang and Shenli Yuan},
journal = {Nucleic Acids Research},
year = {2026},
month = oct,
doi = {10.1093/nar/gkag1038},
url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1038/8986426},
note = {CC BY-NC 4.0},
}
RIS
TY - JOUR
TI - scTHREAD: a cell-resolved long-read transcriptome database with linked isoform, poly(A), junction, and allelic evidence
AU - Zhi-Can Fu
AU - Yelian Yan
AU - Chunchun Wu
AU - Ran Song
AU - Xiaobo Wang
AU - Jianfan Wei
AU - Zhuangzhuang Lu
AU - Tietuo Tao
AU - Peng Lu
AU - Wentao Cui
AU - Yanqiang Li
AU - Keliang Wu
AU - Yong Chen
AU - Tao Huang
AU - Shenli Yuan
PY - 2026
DA - 2026/10/23
JO - Nucleic Acids Research
DO - 10.1093/nar/gkag1038
UR - https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1038/8986426
AB - 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.
SN - 0305-1048
SN - 1362-4962
ER -