I am comparing several genes in mutant vs. wild-type samples across multiple plates in qPCR using ddCt. Can I use one of the same wild-type samples (e.g. WT1) on each plate to do interplate calibration for all samples (both mutant and WT)?
It does not matter what you use as IPC, as long as it is the very same sample on all plates. You can even use a mixture from all your samples or a mix of the standards you produced for assay validation.
You can compare expression of several genes among same samples run on different plates. In each plate, you will test for one housekeeping gene and other target genes. When you calculate the fold expression of each gene for samples run on different plates, you can actually represent data on the same graph and compare from control groups (with a mean fold expression of 1 in each case).
Also, wherever possible, design your experiments so you don't even need to do this.
Because all your comparisons are relative, you are never directly comparing one gene to another (only the differences between samples for one gene, vs the difference between sample for another gene).
If you can load ALL your samples on a plate for ONE gene, do that. Always do that (rather than 'some of your samples, for all of your genes').
Much better to have a single GAPDH plate where every sample is directly comparable with every other sample than to split it and be forced to rely on calibrators.
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