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Open qPCR test run

I recently met up with Ron Shigeta, Ph.D. at Harvard Medical School, and heard him talk to an audience of researchers about IndieBio’s mission. Indiebio is a startup accelerator that focuses on developing early-stage biotech startups. Ron said that Indiebio would be happy to donate an Open qPCR machine from Chai Bio. Naturally I did not pass up a chance for free lab equipment!

The device itself is roughly the same size as one of our smaller non-q-PCR machines. The heated lid contains blue LEDs for fluorescence stimulation, and a sensor for green light below that reads the consequent fluorescence emission during the PCR. This is calibrated by adding a volume of fluorescein to tubes in all of the chambers and comparing the fluorescence of it with distilled water. This will be the basis for all other fluorescence readouts the machine makes during PCR (no pressure). The main downside is that it needs to be recalibrated if the device is moved around too much or the device is used with a different brand of PCR tube. It’s also worth noting that if you’re not careful, fluorescein can and will stain your jeans (learn from my mistake, people).

The Open qPCR connects to a computer so it can record the fluorescence vs. time data. The instrument’s software is open source. You connect to it with a USB cable or even wirelessly, and then use a browser to connect to its internal software. I went with the USB option, although it turned out connecting to the internet is required for setting that up as well. The Open qPCR machine uses the BeagleBone Black, an embedded computer running Linux. The drivers were installed relatively easily. The update had to be installed as an image file. As you can imagine, installing this update was a lot less intuitive than hitting one of those annoying software update prompts. Fortunately Chai Bio’s customer support was quite responsive, especially compared to many other open source pieces of lab equipment. Once we finished installing the drivers, updating the software, and calibrating the fluorescence, we could start designing and running our qPCR experiments.

Like our other not-so-open qPCR machine, the Open qPCR is useful for both real time PCR as well as melt curve analysis. We decided to compare the two machines by running the same protocol on both. We made a simple serial dilution, with samples of pUC19 plasmid ranging from 100ng/uL in concentration, down to 10pg/uL (with molecular grade water as a negative control). The Open qPCR was able to extract Cq values for most of this range, but struggled with the 10pg/uL sample (like our other qPCR did), and distilled water (which would be expected). While they produced similar data, the ramping time for the Open qPCR was quicker. When it came to running 45 PCR cycles of the same protocol, the Open qPCR took about 51 minutes instead of the 1 hour 12 minutes the larger qPCR machine required.

To summarize, the Open qPCR machine is smaller, slightly faster, and has an intuitive user interface. However, it can only process 16 samples at a time (compared to 96 for our other machine), and likely needs to be calibrated more frequently. We’re thankful for Ron and IndieBio donating this piece of equipment.

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