scRNA-seq cell type mapping neuron VS glia proportion

Question

[miyeok]

Hi all,

i am new to this single cell RNA-seq data analysis.

i've done cell type identification of whole brain mouse sample scRNA-seq data.

the results show that all neuron clusters are one-tenth less than glia clusters.

why is that happening? isn't that the neuron ratio almost equals to glia in the brain?

is that just coincidence from single cell library prep?

I appreciate your answers.

Answer 1

[rpolicastro]

Neurons are notoriously difficult to capture in scRNA-seq versus snRNA-seq for droplet based methods (i.e. 10X) because of cell morphology and durability concerns. Some of the newer microfluidics-free methods (like PIP-seq or split-pool combinatorial barcoding) tend to have an easier time capturing neurons in single-cell preps.

[miyeok]

Thank you so much !!