Dear research community

I am planning an RNA-seq experiment of iPSC-derived retinal organoids. The goal is to compare the effects of a gene knockout. I would like to know what would be considered a robust set of replicates in order to draw a convincing conclusion about the differentially expressed genes between the WT and KO group. Here are a few thoughts:

- Should the replicates consist of samples from different differentiation experiments?

- Should the replicates perhaps originate from the same differentiation experiment but from several isogenic knockout clones differentiated in parallel?

- Should the replicates originate from WT and KO clones in different iPSC lines?

- Any other sources of variation that should be taken into account?

I would be grateful if you could share some of you experience from past publications.

Many thanks,

David