Although quantitative PCR uses the same basic concept as traditional PCR, the reactions differ in that the amplicons are generally smaller and are detected indirectly using an additional dye or labeled probe or primer.
dPCR is a relatively new technology and each platform and application has specific requirements (Digital PCR). The protocols are specific for each system and are provided, with excellent support, by the instrument manufacturers. Therefore, the information provided below is a starting point from which specific assays can be developed or optimized.
The Bio-Rad digital droplet system is based on oil emulsification technology and uses a standard 96-well plate format. Each sample is partitioned into 20,000 reactions, yielding a total of 1.9 million reactions per plate. Reactions are set up using Dual-Labeled Probes containing a 5’ fluorescent label and a 3’ quencher, standard to qPCR reactions. The droplet reader is capable of reading end-point fluorescent signals in the FAM and HEX channels allowing reactions to be multiplexed with 2 targets per sample.
A 20× primer/probe mix is prepared as described below. The standard ddPCR master mix is a 25 μL mix that includes the aforementioned primer/probe mix, template DNA and 2× ddPCR super mix.
Samples are loaded into an 8 chamber cartridge using 20 μL of the prepared qPCR sample followed by 70 μL of droplet generation oil in the adjacent wells. A rubber gasket is stretched across the top of the chambers to ensure a vacuum seal. Each 8 chamber cartridge is loaded onto the QX100 droplet generator producing 20,000 droplets per sample. Using a 50 μL multichannel pipette, 40 μL of the generated droplets are transferred to a 96-well plate and heat sealed with pierceable foil. The plate is placed in a thermal cycler using standard 2-step qPCR thermal cycling conditions with a 50% (3 °C/sec) ramp rate. Prior to running thermal cycling conditions, it is recommended to test new primer/probe sets using a temperature gradient to optimize the anneal/extend temperature.
Following thermal cycling, the plate is loaded onto the QX100 droplet reader and end-point reactions are analyzed using Quantasoft™ software.
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