Programming the Opentrons OT-2 robot (opentrons.com) to run protocols (procedures) in biology labs.
This script was produced by Russell Tran for the Guiyan Yan Lab at UC Irvine. The Yan lab studies the relationship between human-made environmental modifications (dams, irrigation, etc.) and malaria, and focuses on Kenya and Ethiopia.
The script uses the Opentrons OT-2 robotics platform to automate Machery-Nagel's "Genomic DNA from Blood" protocol (procedure), published Dec 2015. In brief, the protocol uses various buffers and Machery-Nagel's NucleoMag magnetic beads to isolate DNA from a 200uL blood sample. Should the Yan lab decide to invest in an OT-2 robot, this script would help the lab cut down on the 4-5 hours of manual labor they report it takes them to complete the protocol once (for each 96 samples).
(The protocol has been made to work with Qiagen troughs, though other troughs work too)
- The Qiagen 170 mL troughs have depth of about 52.5 mm, so going to 47 mm deep is a good idea
- The Qiagen 170 mL trough: 7mm height = 30 mL (RECTANGULAR PRISM VOLUME, not that of the trough indent on the bottom)
- Square_wells total depth from the top is 44 mm
- Square_wells meniscus 18 mm from bottom = 800 uL of volume (ratio is 0.0225 mm/uL)
- MBL_3 trough: 12 mm down is sufficient for first "drink" at 170 mL
- 80% Ethanol trough: 30 mm down down is sufficient for first "drink" at 80 mL
- Check if Proteinase K was prepared according to section 3.