Eight till eight

Sunday working was only the beginning of my long working week. Monday was a marathon of a day which had me busy from 8 am right through to 8 pm, and I spent the next day recovering. The good news is that I finally have data! Not that I’ve actually analysed it, but I’m happy to have finally completed a run on the Ion PGM sequencer after many months of waiting. And the fact that it actually worked after the last few chips had failed is even better. My target read length was 200 base pairs, so the PGM sequences these short fragments then aligns them to a reference genome, normally the most recent build of the human genome or in my case, the mitochondrial genome (rCRS). The basis of this type of sequencing is a semiconductor chip with millions of wells on the surface, and each well holds one bead (or Ion Sphere Particle to be precise – ISP for short). The DNA template strands to be sequenced are attached to the ISPs (ideally one type of template molecule per ISP, with many copies). The heat map below gives an idea of chip loading, with blue indicating problem areas and yellow and red indicating good loading.

Loading heatmap of my first Ion 316 chip
Loading heat map of my first Ion 316 chip

Before you get worried unnecessarily, the top left and bottom right are supposed to be blue, but the rest should be as warm as possible. Not too shabby for my first time, if I do say so myself. It may not seem like much, but this is probably the most exciting thing that has happened to me research-wise in the last year!

Source: http://spectrum.ieee.org/biomedical/devices/the-gene-machine-and-me - The best explanation I've found for Ion Torrent technology
Source: http://spectrum.ieee.org/biomedical/devices/the-gene-machine-and-me – The best explanation I’ve found for Ion Torrent technology

Aside from that, I cooked a three course meal, played a significant chunk of the Last of Us, and made a new coin contact. And, I got an invite to the first wave of the Oxford Nanopore MinION Access Programme – essentially a beta test of a cool new sequencing technology. There is a slight barrier in the form of a $1000 deposit, and $250 delivery, but it has great potential as far as publications go. It’s at the cutting edge of biotechnology, and the opportunity to get on board at an early stage is quite exciting. First things first, I’m going to have to convince my supervisor that my cause is worthy and just…wish me luck.



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