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

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!!!

cell single trancriptome
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updated by dsull dsull • written by lidasoltani2050 • lidasoltani2050

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.

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written by dsull dsull

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