Hello, For qPCR to find apoptotic gene activity, it is recommended to collect only live cells. This is because apoptotic cells may have degraded RNA, which can affect the accuracy of the qPCR results.

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For qPCR analysis of apoptotic gene expression, it's recommended to collect both dead and live cells after treatment. This ensures you capture the full picture of gene expression changes related to apoptosis.

Hi.

You must be collected only live cell.

I think the more important question is the genomic material of dead cells active to be used in qPCR?

https://www.researchgate.net/post/In_flow_cytometry_protocol_should_we_wash_the_cells

I share the opinion of Nouhaila Elmoumen; both dead and live cells should be collected and subjected for qPCR analysis

It seems to me that the contradictory advices above point the fact that you will need collect both together, live separately and dead separately (using Kit mentioned in one of answer). Then compare all 3 sets of qPCR data. Although, I doubt that you will get enough RNA from dead cells as it will be considerably degraded and will not be caught by RNA purification Kit.

You don't say what stage of the apoptotic process you are interested in? Pre AnnexinV detection! Post propidium iodide influx? How are you planning to identify and separate your exposed cell cultures to collect your population(s) for subsequent qPCR? Generally, I utilised flow cytometry to identify stages - unstained live cells(fsc/ssc profile), AnnexinV(fairly early apopstosis; all events), AnnexinV/PI(late apoptosis: all events) and PI alone(dead: all events).

You could add fluorogenic caspase substrates to clarify earlier DNA fragmentation stage within the unstained population.