ddPCR for probes to target eDNA samples : from sample preparation to droplet reading v1

The aim of this protocol is the digital droplet PCR (ddPCR) quantification of DNA target(s) using primer and probe sets. This protocol is optimised for the analysis of environmental DNA (eDNA) samples (water, sediment, biofilm and soil matrices) and then rare DNA targets. THe ddPCR can be performed using a QX600 or a QX200 droplet reader system, and this protocol begins after the DNA extraction step and ends with the droplet reading. The ddPCR for probes consists of the absolute quantification of samples using primers and fluorescent dye-labelled probes. The ddPCR technique used is based on the partitioning of samples into droplets by water-oil emulsion and the reading of the DNA signal in each droplet. Multiple eDNA targets can be specifically targeted using multiple primer and probe sets that are compatible. The advantages of using the ddPCR are: the absolute quantification, the sensitivity and the repeatability of the method.