Lessons I've learned NanoSavSeq

  1. The secret that Nanopore doesn't make clear is the requirement (to do anything of importance) of a DNA quantification device, in particular, a qubit. The assay tubes for this device are typically only available through the main site, which doesn't ship to normal people, and the tubes fairly rarely come up on eBay (I grabbed the first bag I could for $100, but waiting for that took well over a week). The qubit device comes up for $500-$1000 every so often on eBay: but the actual operation of it is so simple, I bet that it can be reproduced simply.
  2. RNA degrades pretty quickly. It's absolutely essential to have an ample supply of control in order to actually do experiments, and if your control is degraded to test your primer sets on, you are screwed. I have to find new controls, whether it be synthetic DNA or other, to test my primer sets on because my RNA control has sufficiently degraded so that it cannot be detected anymore.
  3. Do things that don't scale. I optimized this protocol for Opentrons operations, but the tough parts were actually in proper material aquisition. Comparatively, robot protocols are easy.