We had our Flex installed in February, but as yet I don’t have any protocols running reliably.
I’m interested in hearing if anyone has run the following validated protocols with success “out of the box”.
In order of expected difficulty, these are the ones I’d like to run.
- DNA Normalization with Flex 1-channel or 8-channel pipette (https://library.opentrons.com/p/dna-normalization-flex-pipettes)
- AMPure XP 48x (https://library.opentrons.com/p/AMPure-XP-48x)
- Illumina DNA PCR-Free Prep (https://library.opentrons.com/p/Illumina-DNA-Prep-PCR-Free)
- Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus (https://library.opentrons.com/p/Illumina-Stranded_total_RNA_Ribo-Zero)
The Normalization protocol fails to send to the Flex without errors since I updated to 8.4.0, prior to that it would send but I never had a chance to run it.
The AMPure protocol I thought would be such as easy one to get right but that also fails. Sometimes the wells of clean DNA are empty, other times they still appear to have beads still in there. It’s also incredibly slow at near 2 hours for 8 samples. The default 30 minute shaking twice is excessive, and i’m not sure why it’s adding beads twice.
In fairness to Opentrons they have been making modifications to the DNA PCR-Free protocol after I had failures, but it does have a blue check mark so I’d assumed it would just work. The most recent failures are where in a strip of 8 reactions, all wells of final library were empty except one in the middle of the strip, and that had the wrong volume in it. To get it to work i’m told to sit and watch it to see where it loses the sample. This is a relatively short protocol so that’s easily done, but is it truly validated if a user has to do this?
The Stranded Total RNA Prep is one protocol that i’m trying to build up confidence to automate, but it just feels like i’m a million miles away from being able to start a run and walk away from it. If I have to sit and watch this like a hawk for 2 days to check it completes i’m going to lose my mind.
I still have my protocol development credit to use, but I don’t really think I want to use it up to get a “validated” protocol to work reliably.
Please let me know if you’ve used any of these protocols out of the box and had good results.