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icbi-lab / luca

Single-cell Lung Cancer Atlas with 1.2M cells

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Epithelial Cell Types

c-westhoven opened this issue · comments

commented

Hi!

We were wondering what happened to the different epithelial cell types in 33_epithelial_cells

In our project, we are interested in epithelial cells (Goblet cells in particular). Were these cell types filtered out during preprocessing or not found at all?

In the script 33_epithelial_cells.py Goblet cells are mentioned, but the plots aren't visible to give more context.

Thanks in advance!

commented

Hi Charlotte,

there's no reason to expect that goblet cells would be absent. However, t=given the markers I had at hand when I was annotating the cell types I wasn't able to clearly distinguish them form other epithelial subtypes.

One reason for this could be "over-integration" -- Integrating data from different experimental platforms made the integration task pretty hard for scvi-tools and probably led to a reduced resolution. But maybe I just didn't use the right markers and you can find them if you take a look at the epithelial cells yourself.

Cheers,
Gregor