ASE table
Donor-controlled allelic-balance results.
Download TSVscTHREAD: a uniformly reprocessed single-cell long-read transcriptome resource
scTHREAD integrates approximately 450 human and mouse long-read sequencing runs, covering approximately 3.0 million cells and more than 200,000 observed transcript isoforms. Harmonized processing supports comparable views of isoform usage, poly(A) site choice, allelic balance and recurrent novel junctions, with coverage reported separately for each evidence layer.
Statistics
≈450
Sequencing runs
≈3,000,000
Cells
>200,000
Observed isoforms
Human and mouse long-read transcriptomes
Loading biological study descriptions…
Global cell map
Loading the global cell map…
Representative cell-resolved datasets. UMAP is exploratory and does not imply trajectory.
Evidence layers
Gene expression
Available
Isoform
Available
Poly(A)
Available
ASE
Available
Junction
Available
Each result reports the runs and biological units that contribute to that evidence layer.
Transcript & junction browser interactive
Choose a gene to load expression, DIU, APA, ASE and junction evidence.
Scroll over the track to zoom · drag horizontally to pan · select an arc or table row for details.
| Junction | Span | Molecules | Reads | Runs | Studies |
|---|
Cell-type annotation
Gene expression
Validated cell-resolved embedding from long-read gene expression with run-aware integration. UMAP is exploratory and does not imply trajectory.
Live data scope: results report their contributing runs and biological units by evidence layer. Region queries are aggregated on demand and bounded to a 5 Mb window.
Search scTHREAD
Search studies, genes, junctions and genomic regions through the scTHREAD API.
Analyze
Compare evidence across cell types.
Choose a gene or junction, then select from cell-type pairs supported by enough paired biological samples. Ineligible combinations are not shown.
Analyzed
Your comparison will appear here
Results include paired effect sizes, biological-unit counts and exact eligibility boundaries. Unsupported inference is withheld.
Usage prioritization
Estimate pooled junction usage where observation is incomplete.
Predict v1 is cell-type agnostic. It ranks pooled donor-anchored usage for in-domain junctions and preserves observed evidence alongside the score. The score is not a calibrated PSI, biological-validity probability or cell-type-specific effect.
Checking whether a validated model is available…
Predicted
No prediction requested
A validated model may abstain when a junction falls outside its training domain.
Database annotation
Annotate junctions against scTHREAD evidence.
Normalize coordinates and retrieve deterministic motif, recurrence, coverage and sequence/RBP annotations for one junction or a batch.
Ready to annotate
Unmatched and invalid coordinates remain explicit in the output.
Uniform processing workflow
Raw long reads
Human and mouse sequencing runs enter without relying on published aggregates.
IsoQuant
FSM, ISM, NIC and NNC classification with splice-chain reconstruction.
Cell × molecule
Run-aware barcode joins and per-cell UMI deduplication.
Shared evidence
Isoform, PAS, junction and allelic views from one read-facts layer.
Show processing details
Long-read alignments and IsoQuant assignments are harmonized within each run. Gene, transcript, poly(A)-site, junction and allelic evidence use run-aware barcode namespaces; UMI deduplication is applied where molecule tags are available.
Show analysis details
On-demand comparisons merge technical runs into registered biological sample or capture units. The interface offers only cell-type pairs supported by at least three shared units. Allelic balance remains descriptive because haplotype labels are not phased consistently across units.
Download
Sample manifest
One row per sequencing run, with biological context, source accessions, platform, processing state and cell count where available.
| Study | Biological context | Run accession | Species | Platform | Library kit | Cells | Status |
|---|---|---|---|---|---|---|---|
| Loading run-level metadata… | |||||||
About scTHREAD
Loading release metadata from the backend…