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Mouse Pancreas Profile #3

Closed acjordan333 closed 1 month ago

acjordan333 commented 3 months ago

Hi team,

Are there any plans to create a mouse benign pancreas or malignant pancreas profile that can be used for any cosmx experiments run on pancreas cancer mouse models?

Best, Alex

mgrout81 commented 3 months ago

Hello Alex,

Thanks for your interest. No, there are no upcoming plans for non-brain mouse organs. The only CosMx product available for mouse is a neuroscience panel.

m-nayan commented 3 months ago

The CosMx Mouse Universal Cell Characterization Panel (RNA, 1000 Plex) was recently released. Product number: 121500040. https://nanostring.com/products/cosmx-spatial-molecular-imager/cosmx-rna-assays/cosmx-universal-cell-characterization-rna-panel/ https://nanostring.com/resources/cosmx-mouse-universal-cell-characterization-rna-panel-gene-list/

mgrout81 commented 3 months ago

Apologies for the error. There are no current plans to release mouse pancreas reference profiles internally, although we do hope to open this resource to user submissions in the future. The analysis recommendation for mouse pancreas at this time would be to perform unsupervised clustering, and then classify immune cell types using a reference such as one provided here (snRNAseq-based): https://github.com/Nanostring-Biostats/CellProfileLibrary/tree/master/Mouse/Adult.

acjordan333 commented 2 months ago

Ok sounds good. I have tried this as well. It seems that fully unsupervised clustering on mouse pancreas data seems to work OK for now.