What's the point about single-cell sequencing?

Question

[Hashirama]

Dear community,

I have the feeling that there is some hype about single-cell-sequencing. But I don't really understand why this technique is superior over normal RNA-Seq... What makes sqRNA-seq so special? Furthermore, I heard about mass spectrometry as another novel analysis method. Is this even better than single-cell-sequencing?

Answer 1

[rpolicastro]

Single cell sequencing allows you to get genome-wide measurements of RNA/DNA/ATAC/etc. at a per cell level, instead of bulk RNA/DNA/ATAC/etc.-seq that gives you a measurement as an aggregate of all cells used as input. Single cell methods become important when your population is heterogenous (like a tissue) and you are interested in some effect that may be cell specific, such as a developmental pathway or perturbation.

Mass spectrometry is a little different. It's used to measure the abundance of certain peptides, metabolites, and other small molecules in a solution. As an example it can provide the protein levels for a gene in a sample as opposed to RNA-seq which provides the transcript levels. I wouldn't consider them direct competitors, but moreso a set of tools from which you pick the most relevent one for your project. We're even getting to the stage where single-cell mass spec coupled with single-cell RNA-seq is on the immediate horizon, so no choice may be necessary soon (/speculation).