Tested out the plate of Lake Trout primers (LTP01 - forward and reverse combined) for SNP detection. qPCR was performed using Roche 2x HRM M.M. qPCR set up is here. Cycling params are as follows:
95C - 10mins
40 cycles of:
95C - 10s
60C - 15s
72C - 25s
Plate layout matches the primer plate layout.
Results: The following wells have signals and good, clean melting curves: A1, C1, H1, B2, A3, D2, G3, A4, E4, B5, A7, D7, H7, B8, C8, F10, G10, C11, H11, A12, E12. These are potential candidates for SNP analysis. Will test HRM analysis using these primers, each on a subset of Lake Trout DNA samples to see whether or not they’ll be truly useful for analyzing the full plate of DNA.