Exercise 3: How to Fill Plates?

TODO Convert this to h5p

In my qPCR experiment I want to study the pattern of expression of 5 genes (genes of interest and reference genes) in 38 samples (samples of interest and control samples). I want to use 2 PCR replicates for each reaction.

What is the minimum number of 96 well plates I need for this experiment?
5 genes * 38 samples * 2 replicates = 380 reactions.
I need a minimum of 4 plates for this experiment.
If I use the minimum number of 96 well plates do I need to include IRCs?
Yes, 5 genes spread over 4 plates with 72 reactions per gene means that at least one gene will be spread over multiple plates.
What can I do to avoid inter-run variability ?
I can use 5 plates and fill them with one gene each. They will not be completely filled (72 reactions) but at least I do not have to use IRCs (which are additional reactions that also cost money) and I have no inter-run variation.

Suppose there’s only one 96-well plate left in your lab. You have 10 samples (samples of interest + control samples) and you want to make the most of what you have.

How many genes of interest would you measure ?
Since you want to make most of what you have, let’s assume you are omitting PCR replicates. Theoretically, you could fit 9 genes on your 96-well plate. However, to avoid pipetting mistakes I would measure only 8 genes so I can work with one row / gene. This is very handy for multichannel pipets.