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

scTHREAD integrates 453 single-cell long-read runs across 34 human and mouse datasets, profiling 923 389 cells and linking 12 471 531 run-transcript observations to isoform, poly(A), junction, and allelic evidence.

• Why it matters: Cell-resolved transcript structures are needed to compare isoform usage, alternative polyadenylation, and allelic expression across cell types, but existing datasets are fragmented, limiting comparison and reuse.
• What they did: The database uses a uniform, platform-aware workflow to catalogue 12 471 531 run-transcript observations, with 30% linked to 210 341 distinct Ensembl transcript identifiers, while preserving provenance to study, run, and cell type.
• The result: 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.