Guide to reference mapping with Isocortex data from HMB-10X

1

Hi community,

I have some tissues from dorsal lateral prefrontal cortex and I want to use HMB for reference mapping. I see that the Isocortex count data is divided into these region of interest acronyms ‘ACA’, ‘AI’, ‘AUD-TEa-PERI-ECT’, ‘MO-FRP’, ‘MOp’, ‘PL-ILA-ORB’, ‘RSP’, ‘SS-GU-VISC’, ‘VIS’, ‘VIS-PTLp’. But it is not clear to me what these acronyms represent. Some of these acronyms are not defined in the paper, so these are literally black boxes. I suppose these are related to the CCFv3 coordinate systems? Not sure. Anyone can elucidate where I can find more about these acronyms and which region should I best use to help reference map my dlPFC data?
Any tips would be much appreciated.

Best,
JC

2

Hi, found what I was looking for in the first supplementary table 1 from the paper. Hopefully this helps.

3

This acronym list might help as well: https://brainmapportal-live-4cc80a57cd6e400d854-f7fdcae.divio-media.net/filer_public/c8/42/c8421c8e-72d8-4781-8505-8770e88671a7/whole_mouse_brain_acronym_june_2024.xlsx

This is the “Whole Mouse Brain, Acronym List” from Cell Types Support: Guides, Tutorials, SOPs, and Helpful Links - brain-map.org