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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 of sample and primer required.

Primer Sets Samples
NumberVolume of sampleNumberVolume of sample
12 4.5ul x4 wells384 3.0ul
24 4.5ul x2 wells216 3.1ul
36 5.1ul 144 3.3ul
48 4.5ul 108 3.5ul
54 4.3ul 96 3.6ul
72 3.9ul 72 3.9ul
80 3.8ul 64 4.1ul
96 3.6 54 4.3ul
120 3.5ul 42 4.8ul
144 3.3ul 36 5.1ul
216 3.1ul 24 4.5ul x2 wells
248 3.1ul 20 4.9ul x2 wells
296 3.0ul 16 4.1ul x4 wells
384 3.0ul 12 4.5ul x4 wells

Wafergen recommends samples normalized to a concentration of 10 ng/uL. Although normalization is not required, the minimum acceptable concentration is 1 ng/uL.

Primers should be reconstituted to a concentration of 1.5 uM.

Also required are two Excel spreadsheets detailing the names of the samples and the primers, respectively, arranged in the order they will be dispensed.


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 (there is a higher cost associated with this). 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 (




Each chip currently costs $150.
Training runs will cost an additional $100 for the first three runs.
384 plates specific for the Wafergen system (two required) are $10 each.

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