Data · dataset · 2024
Spatiotemporal transcriptomic map of glial cell response in a mouse model of acute brain ischemia
Listed in Teesside University Research Data Repository
Hello, Welcome to the repository for the processed data objects for our manuscript titled "Spatiotemporal transcriptomic map of glial cell response in mouse model of acute brain ischemia" published in PNAS (doi: 10.1073/pnas.2404203121).
Description
In this study, we used spatial and single-cell transcriptomics to map out processes governing the response to ischemic stroke during the first week after the injury. Focusing on glial cells, we documented their activation, formation of glial scar and changes in cell-cell communication patterns.
Here, we list seurat objects of the spatial and single-cell experiments. List of files: - seurat_1stSpatial.rds. A seurat object with Visium ST generated data (gene expression matrix, metadata and image).
Read the rest (2 more)
Clean, suitable for starting-anew analysis. - seurat_2ndSpatial.rds. A complementary seurat object to the seurat_1stSpatial.rds. - spatial_seurat_1DP_13_nygen.rds. A complete seurat object of the final Visium spatial dataset (modules scores, deconvolution, ligand-receptor pair values...) - Seurat_sn_MCAO_Zucha2023_QCFiltered.Rds.
Seurat object of pre-processed single-nucleus data. - Seurat_OLs_integrated_annotated.Rds. Seurat object of processed oligodendrocyte data integrating the single-nucleus and single-cell experiment. Corresponding author contact: lukas.valihrach@ibt.cas.cz
Links
Where it is published
- DOI doi.org/10.17632/gnb2dsjms2.1 ↗
DOI / persistent id · from researchdata tees ac uk
Catalogue records · 1
- OAI-PMH record data.mendeley.com/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=oai%3Adata… ↗
metadata API · from researchdata tees ac uk
Topics
- From keywords
- Computational neuroscience · Earth & Environmental Science · Engineering · Humanities · Life Sciences · Social Science
- Inferred from text
- Image 75%
Provenance · 1 source records, 12 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| Teesside University Research Data Repository | oai:data.mendeley.com/gnb2dsjms2.1 | 5 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| concepts[field].anzsrc:field:320904 | mapping · researchdata tees ac uk | vocabulary-mapper@1.0.0 | keywords['Computational Neuroscience'] |
| concepts[field].local:field:earth-environmental | mapping · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| concepts[field].local:field:engineering | mapping · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| concepts[field].local:field:humanities | mapping · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| concepts[field].local:field:social-science | mapping · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| concepts[modality].local:modality:image | enrichment · researchdata tees ac uk | keyword-concept-rules@1.0.0 | title+description (75%) |
| description | source · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | /metadata/dc/description |
| license | source · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | /metadata/dc/rights |
| publication_date | source · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| title | source · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | /metadata/dc/title |