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🐛 Need list of cell types that are not supposed to be in organ model #106

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andreasbueckle opened this issue Sep 4, 2024 · 1 comment
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@andreasbueckle
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andreasbueckle commented Sep 4, 2024

The popV crosswalk lists hepatocyte as a cell type in the heart. However, they should only appear in the liver. We need to check if there are more cell types in the wrong organ model in the popV crosswalk.

PS: This causes downstream issues, such as wrong cell types showing up in the FTU Explorer: to hubmapconsortium/hra-ui#615
PPS: This is also captured in hubmapconsortium/hra-workflows-runner#37

@emquardokus
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The main reason we can NOT have a table that lists "Need list of cell types that are not supposed to be in organ model" because some cell types like various immune cells will always appear in all organs---different numbers or specific immune cells.
The hepatocyte example is the only one we found because it's such an obvious mistake---hepatocytes should only be in liver not heart or lung.
The other possible issue is if a sample block had contaminating tissue from surrounding organs---example: liver is in close proximity to both heart and lung. In this case, one would expect that the number of these contaminating cell types in a dataset should fall below the threshold one would expect of cells that natively exist in the primary tissue. This is one of the preprocessing steps for single cell RNA sequencing analysis--- remove cells that are 3 or below. This threshold can be modified during the analysis.

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