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
Find a dataset or gene.
Choose a species first. Then open a dataset directly or search by biological context, gene, accession or coordinate.
Species
Choose by biological source
Labels describe tissue, disease or cell line; accessions remain available in the results.
Enter what you know
Choose a dataset above, or try one of the example searches.
Analyze
Compare cell types.
Test whether a gene uses different isoforms or poly(A) sites between two cell types. Only comparisons supported by paired samples are offered.
Comparison
Choose two cell types
The result will show which transcript feature differs and how many paired samples support the comparison.
Junctions
Check a splice junction.
See whether it was observed, where it recurs and whether it uses canonical splice sites.
Ready
Results will show observation, recurrence, splice motif and supporting molecules.
Optional model estimate
For one junction, estimate pooled usage when measured coverage is incomplete. A higher score means the model ranks it closer to frequently used junctions; it is not a probability and does not compare cell types.
Checking model availability…
No estimate requested
Out-of-domain junctions return no score.
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…