What is the standard of validating differentially expressed genes experimentally from scRNA seq analyses?

Question

[yojetsharma]

Are we required to carry out ddPCR to validate the DGEs obtained from scRNA seq analyses?

[seidel]

You could do in situ expression analysis if any of your cell types are available via histology. Sometimes people make GFP or mCherry reporter constructs to show expression in a given cell type. It sort of depends on what tools are available for your system and how much you want to say about your results.

Answer 1

[ATpoint]

There is no standard if you ask me. I cannot recall a single-cell paper doing qPCR. If you want to validate markers then rather do immuno/protein confirmation or FACS. For qPCR would need to isolate cells first via FACS anyway so why bother. It's imo an overrated assay with many drawbacks and little power.