The QuantStudio 7 along with the Taqman chemistry can be used for both genotyping and gene expression analyses that are focused on a smaller number of samples, SNPs and genes of interest. The system can be used on a per-run basis by users who wish to prepare their own plates. We currently only run samples in 384-well plates.
TaqMan assays are based on 5' nuclease assay in which the PCR amplification and genotyping or gene expression profiling are combined in one reaction. For genotyping studies, the genotypes of the SNPs are determined by comparing the fluorescent signal for each of the two allele-specific reporter dyes following amplification. For gene expression profiling, the fluorescent signal from the amplification products can be compared against a standard series that is included with the experimental assays for absolute quantitation or against the signal from another sample for relative quantitation.
A quick reference guide for the instrument is available here. Experimental setup starts from p.4.