Lab Automation at Addgene

By Shannon Rinaldi

Updated Apr 6, 2021.

If you’re doing high throughput work, it’s likely that you come into the lab wishing there was a machine that could make your life a hundred times easier. We’ve certainly felt this way at Addgene so we’ve been putting some work into finding robots that’ll take a little labor off our hands.

Good news! There is probably a machine or robot out there that does exactly what you want plus way more than you thought it could ever do! However, there is quite a bit of upfront research you have to do to find said robot and to find out how you can get one. As a starting point, I would recommend conferences like Lab Robotic Interest Group (LRIG). There is so much to see and so many more robots than you ever knew existed!

Addgene recently started automating a few protocols to make standard lab processes easier and more efficient. Here, I’ll discuss transformation, DNA purification, and filling vials with agar. I’ll also provide you with some tips on how to automate some simple processes in your own lab.

Automating bacterial transformation

One protocol that has been automated is high throughput transformation. With our ever growing rate of plasmid deposits (over 100 deposits per month!), manual transformations were taking a lot of time.

Enter the Biomek FXP!

We wanted a machine that would improve our transformation protocol and, after looking at a few options, we decided on Beckman Coulter’s Biomek FXP. We had a previous relationship with Beckman Coulter and that certainly played a factor in our decision to go with this machine, but we also really liked that Beckman was flexible and willing to make removable parts to fit on the deck of the Biomek. The FXP id also able to do high throughput DNA preps and other molecular work if we need it to. This gives us the oppotunity to use the FXP to automate and optimize more protocols in the future - something that will be key for our future growth.

One of the biggest benefits of the Biomek FxP is it’s customizability. It has a large deck that can house many different types of devices. As long as a device fits on the deck, and it’s easy to pipette samples in and out of it, you can set up a procedure for it using the Biomek FxP. For example, we added a cooling block to our set up. The cooling block is used to keep our cells from warming up too much and dying.  Also, we added a couple of platforms that fit 48 well q- trays allowing us to do up to 96 transformations in one run compared to doing about 50 transformations in the same amount of time by hand!

Setting up a basic protocol on the Biomek FxP is pretty simple. By clicking a few buttons you can quickly tell the Biomek FxP how much sample to pick up, where to move it, and how long to keep it there. In addition, the FxP has two robotic, mobile pods - one pod can pick up 96 tips for easy sample transfer between 96 well plates. The second pod can pick up 8 tips and position the tips indepently making it easy to spread out your samples. This can be useful if you’re transferring samples from 96 wells plates onto agar q-trays where the samples must be spread much farther apart before plating. With this fine piece of machinery we have been able to transform 96 samples in about 4 hours with a greater than 95% success rate!

Automating DNA purification

We're developing ways to prep large quantities of DNA because some countries just can’t receive bacteria through the mail due to laws concerning genetically modified organisms. Since Addgene is very proud to help scientists share plasmids across the globe, we’re working on ways to send plasmids as DNA as opposed to in live bacteria. For these shipments, we’ve needed to find a way to purify DNA from many bacterial samples at the same time as opposed to preparing each sample individually.

Enter the BIOROBOT!

This robot is called the Qiagen BIOROBOT Universal Platform and it suits our plasmid prepping needs perfectly. Working with Qiagen, we developed a protocol to run up to 192 samples at a time. It follows all the same steps and uses the similar buffers as would be used for a mini prep, except it does it on a larger scale. Using the BIOROBOT Universal Platform is ideal because it eliminates the potential of human error or cross contamination between samples. With this automated protocol, we can prep two 96 well plates in just under 3 hours or one 96 well plate in about an hour.

Automating vial fiIling

The majority of Addgene plasmids are shipped as agar stabs in glass vials. Have you ever wondered who fills all those vials? Well, it used to be a lab assistant, but with increased plasmid demand it was too time consuming to complete this process by hand and we welcomed yet another robot onto the lab team.

Enter the Liquid Handler!



This machine fits on a table top and can be easily programmed for a variety of lab needs. Addgene uses it to fill as many vials as it can in the shortest amount of time. Racks of 48 vials are set up on the bed of the Liquid Handler and we program the handler to fill a specific number of vials with a specific amount of agar. There is a tube that goes from the needle to the flask with agar in it. The agar sits on a hot plate with a magnet so that the agar doesn’t solidify while it goes through this process. With enough agar and the right program, the liquid handler can fill 400 vials in 35 minutes compared to a lab assisstant filling about 200 vials in 45 minutes by hand.

How can you start automating your lab?

You might not be doing enough transformations, minipreps, or filling enough vials to automate these processes, but there are many simple steps you can take to automate processes in your own lab. Some things your lab can do to get into the robotics spirit include:

  1. Start using electronic multichannel and single channel pipettes. These can speed up any project in which you need to do a lot of aliquoting. Simply program the pipette with how much total sample you need and the volume of the smaller aliquots you’d like to dispense and you’re on your way.
  2. Label your tubes with a label maker. Label makers generate far more legible labels than your hand and help keep things more organized.

    barcode on a glass vial for plasmid stabs
  3. Cap tubes with a micronic cap sealer. This is a simple table top device that has a roller to go over caps and push them into micronic tubes instead of pushing them in one by one. It seems very simplistic and it isn’t electronic but it is one of the most helpful machines I have used in the lab. It’s especially useful if you want to avoid sore fingers.

    micronic cap sealer

There are other process that Addgene would love to move forward and automate. For instance, vial labeling would be much easier with a Tube Writer, which air brushes the information onto the vials instead of requiring us to put a label on each tube by hand. We’ll be sure to tell you about more lab updates as we develop them. In the meantime, if you have any great lab automation tips and tricks, be sure to share them in the comments section.


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