How can you separate and ignore the expression changes caused by single cell isolation from the single cell transcriptome ?

Question

[lidasoltani2050]

Hi everyone

In single-cell RNAseq.. isolating a single cell is a process that can alter the expression of the cell's genes at that moment... is this an effect that limits our experiments, or is this the reason for a biased transcriptome? Can the isolation of a single cell have a negative effect on our experiment?

because I think this isolation can have a strong impact on expression. And besides the expression caused by the defined experimental conditions, we also have an expression change caused by the mechanical isolation of the single cells!!!

[dsull]

Is there evidence that this will have a “strong” impact on expression? When I’m working with PBMCs, I’m sure my T cells won’t start looking like B cells because of this isolation… More seriously, the treatment will affect all cells so your experiment won’t be confounded. And if you’re trying to compare isolation technologies versus non-isolation technologies (like bulk RNAseq), you probably have more batch effects to worry about than the isolation procedure.

In any case, if this is a concern of yours, you can try a technology like split-seq which starts from cross-linked cell pellets.