Data · dataset · 2026
Spatial transcriptomics data
Listed in UP Research Data Repository
<p dir="ltr">This dataset contains AlphaSpatial-predicted cell-level gene expression and spatial coordinates for two breast tissue sections, 187 cases from the Yale HER2-status cohort and 81 cases from the Yale trastuzumab-response cohort.
Description
The archive comprises 270 AnnData files containing 14,594,148 valid cell predictions, together with an ROI mapping table. Each file provides untransformed predicted gene counts, gene identifiers, cell coordinates and available ROI and inference-quality metadata.
The mapping table links Yale ROIs to their source slides and annotation geometries. These data support analyses of stromal organization, HER2-associated molecular and spatial patterns, and treatment-response-associated microenvironments. Expression values are model predictions rather than experimentally measured transcript counts.
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Original histological images and model weights are not included.</p>
Links
Where it is published
- DOI doi.org/10.6084/m9.figshare.34060014.v1 ↗
DOI / persistent id · from researchdata up ac za
Catalogue records · 1
- OAI-PMH record api.figshare.com/v2/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=oai%3Af… ↗
metadata API · from researchdata up ac za
Topics
- From keywords
- Bioinformatic methods development · Earth & Environmental Science · Engineering · Humanities · Life Sciences · Social Science
Provenance · 1 source records, 13 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| UP Research Data Repository | oai:figshare.com:article/34060014 | 4 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · researchdata up ac za | connector:researchdata_up_ac_za@1.0.0 | |
| concepts[field].anzsrc:field:310201 | mapping · researchdata up ac za | vocabulary-mapper@1.0.0 | keywords['Bioinformatic methods development'] |
| concepts[field].local:field:earth-environmental | mapping · researchdata up ac za | connector:researchdata_up_ac_za@1.0.0 | |
| concepts[field].local:field:engineering | mapping · researchdata up ac za | connector:researchdata_up_ac_za@1.0.0 | |
| concepts[field].local:field:humanities | mapping · researchdata up ac za | connector:researchdata_up_ac_za@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · researchdata up ac za | connector:researchdata_up_ac_za@1.0.0 | |
| concepts[field].local:field:social-science | mapping · researchdata up ac za | connector:researchdata_up_ac_za@1.0.0 | |
| concepts[modality].local:modality:image | enrichment · researchdata up ac za | keyword-concept-rules@1.0.0 | title+description (65%) |
| concepts[modality].local:modality:tabular | enrichment · researchdata up ac za | keyword-concept-rules@1.0.0 | title+description (65%) |
| description | source · researchdata up ac za | connector:researchdata_up_ac_za@1.0.0 | /metadata/dc/description |
| license | source · researchdata up ac za | connector:researchdata_up_ac_za@1.0.0 | /metadata/dc/rights |
| publication_date | source · researchdata up ac za | connector:researchdata_up_ac_za@1.0.0 | |
| title | source · researchdata up ac za | connector:researchdata_up_ac_za@1.0.0 | /metadata/dc/title |