I will start with retina organoids culture. According to your experiences, is it possible to extract RNA (cDNA) for qPCR from a single organoid?. If it's the case, which method you recommended?
Do you know how many cells are in your organoids or what they weigh? I usually get around 1 microgram of RNA per milligram of mouse brain tissue, and I'm guessing the expected yield from an organoid would be fairly similar. The range of expected RNA yields per milligram of animal tissue is usually written in RNA extraction product/kit documentation. You could use this to estimate how many organoids you'll need to get the amount of RNA required for your downstream experiments.