Hi! I have performed bulk hippocampal transcriptomics in mice and I’m interested in performing deconvolution to separate the different cell types. Is there a suitable database which I can use as my matrix and which method of deconvolution would you recommend? Thank you!
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ABC atlas can serve as a good reference for your study. You can find instruction for accessing the data here: GitHub - AllenInstitute/abc_atlas_access: Documentation and examples demonstrating how to access data from the Allen Brain Cell Atlas
Particularly, cellxgene matrix and metadata for HPF (hippocampal formation) can be found here:
You might want to further subset based on roi information, or by cell types based on their spatial location determined by MERFISH.
We don’t have much hands-on experience with the bulk deconvolution, so couldn’t give you much advice. You might find this website useful, which provides substantial resources on this topic: