The Opentrons Magnetic Module is designed to automate magnetic bead based protocols on the OT-2. The magnetic module (sometimes referred to as the "MagDeck") is compatible with most magnetic bead kits on the market, allowing biologists to automate nucleic acid purification protocols including PCR clean-up, genomic DNA extraction, plasmid purification, RNA extraction, and more. 

This article goes through:

  1. Compatible labware 

  2. Installing the Magnetic Module on the OT-2

  3. Creating a protocol using the Magnetic Module

  4. Calibrating a protocol using the Magnetic Module

  5. GEN1 vs GEN2 

Compatible Labware

See: What labware can I use with my modules?

Installing the Magnetic Module on the OT-2

1. Place module on the deck. 

The Magnetic Module fits directly onto slots on the OT-2's deck.

For guidance and recommendations on where to place your Magnetic Module, see our article on module placement on the OT-2.

The Magnetic Module requires two different connections, one to the power source and one to the OT-2 for control by the robot. The pronged jack is the power cable and the USB Type-A goes into the USB port in the back of the robot. 

The power cable connects directly to a large power supply brick that plugs into the wall power outlet. The control cable goes to the USB sockets in the top left corner of the OT-2.

Use the cable holders on the side of the robot to keep the USB cable out of the way. 

3. Power On & Check Connection

Press the small black button to power on the Magnetic Module. You should hear some small motor noises as the module homes itself on boot. 

Now your robot should be able to see that it has a MagDeck connected to it. Open the Opentrons App and connect to your robot over USB or Wi-Fi. Then, you can click on the PIPETTES & MODULES tab below the name of your robot. You should see the pipettes and modules connected to your robot, as in the screenshot below:

Note: The PIPETTES & MODULES tab also displays the serial number below each detected module. Alternatively, you can find the serial number of your module by looking on the bottom of the physical device. There will be a sticker with letters and numbers.

Using your Magnetic Module in OT-2 Protocols

You can incorporate your Magnetic Module into your Python API or Protocol Designer protocols.

  • Learn about using your Magnetic Module in Protocol Designer protocols here. Protocol Designer support for modules was introduced in software version 3.17, in May 2020.

  • Request a custom protocol by using the Opentrons Custom Protocol Development Request Form.

  • You can also find some protocols using the Magnetic Module on our Protocol Library.

  • Read on or go directly to our API documentation to learn about using a Magnetic Module in a Python API protocol.

Calibrating a Protocol with the Magnetic Module

Before you calibrate your labware with your Magnetic Module, Opentrons recommends ensuring your labware locks to the module by adjusting the black plate bracket on top of the module.

Please note there are two sizes of plate brackets supplied with your module: Standard and deep well. These brackets can be removed and swapped by unscrewing the module's thumb screw (silver knob on front):

When you have completed your protocol using the MagDeck, it is time to load it into the Opentrons App and run it.

The robot will be able to see that your protocol includes a MagDeck and will check to make sure that it is connected. It will then display the module in the deck slot the protocol you assigned to the MagDeck (Slot 1 in the example below). You can then proceed through labware calibration in the same way you normally would. The robot will move to the A1 location of the plate on top of the MagDeck for you to save the position in the same way as it does for every other labware.

Once you have completed your calibration, you can run your protocol! 

GEN1 vs GEN2 Magnetic Modules

How to tell if which generation of module you have

GEN1 magnetic modules have long magnetic bars. The GEN2 modules have numerous, shorter magnetic bars. 

A GEN1 magnetic module (pictured left) and a GEN2 magnetic module (pictured right)

When switching between generations there are a couple things to keep in mind. 

  1. There will be a difference in incubation time. The magnets on the GEN2 module are more gentle. Because of this, if you are changing a protocol to use a GEN2 module instead of a GEN1 module, you may need to increase the time you wait for the magnetic beads to settle into place. Please experiment with time to see what works best with your module and beads. 

  2. There is a difference in how engage height is represented. The units for GEN1 module engage height were not based on a standard unit of measurement. Engage height for GEN2 modules is in millimeters. 

Converting engage height between generations

  • To convert engage height from GEN1 to GEN2, divide by 2. 

  • To convert engage height from GEN2 to GEN1, multiply by 2.

  • If you are using the Protocol Designer, compatible labware, and have not changed any of the default engage heights in your protocol, this conversion will be done for you automatically when you switch generations. 

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