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Image of Wafergen's SmartChip
Image of Wafergen's SmartChip

The Wafergen SmartChip System is a highly flexible nanoliter qPCR instrument. The system is based on aluminum chips that contain a grid of 72x72 nanowells. Each well can hold up to 150ul of volume. The system itself is composed of two halves: a robot for loading the chips and a PCR machine for cycling and scanning the chips.




Wafergen reactions come in two flavors: prefilled arrays and "MyDesign". Prefilled arrays have specific primer sets laid out across the nanowells. MyDesign arrays are filled in two steps: cDNA followed by primers.

Primers and cDNA are filled from specific 384 well plates in master mix already diluted to 1x. Technical replicates must be pipetted the desired number of times on the plate. eg. if you want to run your primers 3x on the cDNA, you should use 3 wells for each primer set and only 1 for each cDNA. Even though each dispense uses only 50nL, more material is required for pipetting. The matrix below outlines the preprogrammed sample:primer set ratios and the volumes required.

Samples Primer Sets
Number Volume Number Volume
12 18ul x4 384 12ul
24 18ul x2 216 12.5ul
36 20.5ul 144 13.5ul
48 18ul 108 14ul
54 17.5ul 96 14.5ul
64 16.5ul 80 15.5ul
72 16ul 72 16ul
80 15.5ul 64 16.5ul
96 14.5 54 17.5ul
108 14ul 48 18ul
144 13.5ul 36 20.5ul
216 12.5ul 24 18ul x2
384 12ul 12 18ul x4

Primers should be at XX concentration in 1x mastermix. cDNA should also be in 1x Mastermix.


Image:BioMicroCenter-WafergenRobot.png The Wafergen system is offered as a walkup service in the BioMicro Center. However, due to the complexity of the Wafergen system, a single brief training session is not sufficient for us to be comfortable letting users operate on their own. Instead, new users must use the robot under the guidance of the BioMicro Center technician for the first 2-3 runs. Once the user has completed their guided usage, you are free to use the system without supervision.

Users may sign up for the Wafergen system on the calendar‎. New users should confirm their schedule with BioMicro Center staff (




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