What is the reason that all high throughput sequencing data for the human brain is snRNA-seq instead of scRNA-seq ?

Question

[JACKY]

I was looking for scRNA-seq data from healthy human brain tissue—nothing specific, just any part of the brain would do—but I couldn't find any at all! It made me wonder: why is this the case?

Is snRNA-seq really that much better suited for brain tissue? What are the advantages of using snRNA-seq in this context?

Answer 1

[jared.andrews07]

Brains are incredibly difficult to dissociate. They're like a huge tangle of wires given all the axons, myelin, etc. While you can do single cell RNA-seq on brain tissue, it will skew which cell types you get out - it'll be heavy for glial cells while most of the neurons will just get shredded. Most of the neuronal pops you retain will be immature neuroblasts or neural precursors/progenitors depending on the age of the tissue. Brains have expansive and prolonged post-natal development in humans and mice, so the cell types you can expect to get out depends on that.

Nuclei isolations, while still difficult (especially from mature tissue), let you better remove a lot of the extraneous protein/debris and retain populations of interest.