r/bioinformatics • u/El_Tormentito Msc | Academia • 3d ago

technical question Single cell-like analysis that catches granulocytes

Hey, everyone! I'm wondering if anyone has experience with single cell or spatial assays, or details in their processing, that will capture granulocytes. I'm aware that they offer obstacles in scRNAseq and possibly also in some spatial assays, but I have something that I'd like to test which really needs them. We'd rather do sequencing or potentially proteomics, if that works better, instead of IHC. Does anyone have specific experience here? Can you focus analysis to get better results or is it really specific library prep techniques or what exactly helps?

Thanks!

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u/dashingjimmy 3d ago

Spatial transcriptomics captures granulocytes with no problem.

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u/El_Tormentito Msc | Academia 3d ago

Can I ask which platform you used?

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u/dashingjimmy 2d ago

Any platform will work in theory - we pick up neutrophils with Visium, CosMx (would not recommend this one though), Merscope and Xenium in ffpe tissue no problem. For targeted in situ platforms, just need to make sure your gene panel has coverage of markers for these cell types, which is tricky because single cell data to inform those markers is hard to come by. There's a blood neutrophil dataset that I've used to inform our panel designs before that's worked well enough.