Mouse Cortex Cell types

[sthawinke]

Thanks a lot for making all data available here.

I have a question on matching in the "SpatialNF/examples/data" folder. How can I match the cells in _mouse_cortex_molecularcartography to the cell types in _referencescRNAseq? In the former there is a "parent_cell" identifier, but where do I find this identifier in the referecne scRANseq data?

Thanks a lot!

[heckern]

Inside the 'examples/data' folders are only input files; not the resulting the cell type mappings. The 'parent_cell' just refers to the segmented cell in the spatial data where the transcript is located (not really important).

To get cell type mapping scores, you can run one of our Tangram Nextlow pipeline:
https://github.com/aertslab/SpatialNF/tree/main/examples/tangram

If you are interested in the annotated mouse cortex molecular cartography data, we used it in our SCENIC+ manuscript: https://www.nature.com/articles/s41592-023-01938-4

You can find the A1 slice in this SCope session under 'Mouse_cortex_TEW' --> 'Resolve': https://scope.aertslab.org/#/scenic-v2/*/welcome

Hope that helps