Unexplained Cell Type Annotations

[guarelin]

Hi!

Thank you for this awesome dataset resource! There are a few cell type annotations I can't find in the paper, and after poking around the code, I'm still having a hard time defining them.

Namely:

• hormones cell types for the endometrial cells/nuclei
• eM cell types for the immune cells/nuclei

I could be missing something, but I would appreciate it if you can point me in the right direction.
Thank you!

[guarelin]

Note - answered my own question via the supplement.

Supplement PDF

Hormones cell types - clusters of epithelial or mesenchymal cells from donors on exogenous hormones.

I still can't find info on the eM cell types though. There are 16 nucleus cell types in the figure at the bottom of this notebook:
Immune Nuclei MILO

But there are 18 nucleus cell types in this figure:
Extended Fig 8

In notebook but not figure:

• eM1, eM2
• these are also found in the h5ad data relase

In figure but not notebook:

• uNK1_cycling
• plasma B cell
• uM1, uM2, uM2_cycling

To me it seems like eM1 and eM2 were renamed in the paper to uM1 and uM2

[luzgaral]

Hello,

Apologies eM (endometrial Macrophage) and uM (uterine Macrophage) are the same. So it is correct that eM1 and eM2 were renamed in the paper to uM1 and uM2. We will update our annotated objects to avoid further confusions.

Also note (i) Plasma B or uNK1_cycling cells are only detected in the single-cell (sc) or single-nucleus (sn) datasets, so keep this in mind; and (ii) MILO was run on the sn dataset to avoid technical batch effects introduced by different labs profiling the sc datasets.

Hope this makes sense. Please get in touch if you have any further question.

Best,

Luz