[BUG] Bone marrow cell annotation in Tabula Muris Senis 10x

[bfurtwa]

The cell_type labels in the Tabula Muris Senis bone marrow 10x datasets seems to be mixed up.
In the UMAP you can see cell_types clustering together that are very unlikely to be similar.
I plotted some markers for the different lineages that show that the cells cluster correctly, but are wrongly annotated.
Markers by row:

1. Erythropoiesis
2. Granulopoiesis
3. Monocytopoiesis
4. Stem and niche cells
5. Endothelial cells and Pericytes
6. Lymphopoiesis
7. Megakaryocytes

[jahilton]

@bfurtwa Thank you for bringing this to our attention. We have made the contributors aware of your question.

Can you explain where you obtained the file that your plots were derived from? The CELLxGENE Discover version of the 10x Bone Marrow Dataset does not have obs.cell_ontology.class (though, it does show the same cell population metadata based on obs.cell_type)

[bfurtwa]

I got the file from here:
https://figshare.com/articles/dataset/Tabula_Muris_Senis_Data_Objects/12654728?file=23873090

It seems to be the same as here:
https://cellxgene.cziscience.com/e/0bd1a1de-3aee-40e0-b2ec-86c7a30c7149.cxg/

[bfurtwa]

It seems like this issue has already been resolved by the contributor, so the correct datafile should be out there somewhere.
czbiohub-sf/tabula-muris-senis#4

[jahilton]

The contributors are looking into this, so hopefully we get it resolved soon (though likely after the holidays)