Can I estimate RNA velocity in Visium Spatial Gene Expression for FFPE

Question

[oghzzang]

Dear USERs,

I have following question. Can I estimate RNA velocity in Visium Spatial Gene Expression for FFPE?

To estimate RNA velocity, we need to calculate the unspliced & spliced RNAs in a gene. I did it using velocyto program. But, they couldn't do it.

So, can we obtain the unspliced/spliced RNA correctly from Visium for FFPE (v2)?

https://cdn.10xgenomics.com/image/upload/v1666737555/support-documents/CG000605_GenomicDNAinVisiumCytAssistSpatialAssay_RevA.pdf

Answer 1

[ATpoint]

No, Visium uses probes that exclusively (to my knowledge) binds exons, so no unspliced counts from that assay.

[oghzzang]

Thanks for your help!

[dsull]

A fun experiment might be to see how many unspliced counts you get (probably not many at all -- but still would be cool to check since exons are also part of unspliced RNA). Edit: Maybe I'll try this analysis myself in the next week or two since I'm working on a similar project.