Using the Oxford Nanopore
New to topics? Read the documentation here!
With all this ready, we opened the Nanopore flow cell, which is the 500 dollar consumable piece that goes in the sequencer.
We then had to pipette the final golden Eppendorf into the flow cell. My anxiety levels were going through the roof: Figure 4. "Oxford nanopore MinION flow cell pipette loading.".
At this point bio people start telling lab horror stories of expensive solutions being spilled and people having to recover them from fridge walls, or of how people threw away golden Eppendorfs and had to pick them out of trash bins with hundreds of others looking exactly the same etc. (but also how some discoveries were made like this). This reminded Ciro of: youtu.be/89UNPdNtOoE?t=919 Alfred Maddock's plutonium spill horror story.
Luckily this time, it worked out!
We then just had to connect the MinION to the computer, and wait for 2 days.
During this time, the DNA would be sucked through the pores.
As can be seen from Video 1. "Oxford Nanopore MinION software channels pannel on Mac." the software tells us which pores are still working.
Pores go bad sooner or later randomly, until there are none left, at which point we can stop the process and throw the flow cell away.
48 hours was expected to be a reasonable time until all pores went bad, and so we called it a day, and waited for an email from the PuntSeq team telling us how things went.
We reached a yield of 16 billion base pairs out of the 30Gbp nominal maximum, which the bio people said was not bad.