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JEFworks-Lab / STdeconvolve

Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data
http://jef.works/STdeconvolve/
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Question about STdeconvolve: MOB layer transcriptional profiles #55

Open ZZYMaxwell opened 2 months ago

ZZYMaxwell commented 2 months ago

Hi，@bmill3r，

I recently read your paper "Reference-free cell type deconvolution of multi-cellular pixel-resolution spatially resolved transcriptomics data" and found it very insightful.

I tried to replicate the results of the MOB dataset using the code shared on GitHub and got good results. But I have a question: the transcriptional profiles of different layers of MOB were provided on github. How did you calculate these transcriptional profiles? Where can I find the corresponding single-cell data set about layer transcriptional profiles?

bmill3r commented 2 months ago

Hi @ZZYMaxwell,

So sorry for the delayed response. You can find more information on how the MOB data was processed in the supplementary methods of the paper. Briefly, unsupervised clustering was performed resulting in assignment of capture locations to 5 distinct clusters, which we then manually annotated based on the location of capture locations on the MOB tissue section. To get the transcriptional profile for a given cluster. we can take the average gene expression across capture locations belonging to a given cluster. I believe the test dataset available on GitHub is MOB sample #8 from the study we collected the data from.

Hope this helps, Brendan