Ancient hominids, get your DNA cleaned up here!

15 June 2013 by Kerstin Hoppenhaus, posted in Ancient DNA, Genetics

Marie is back in the cleanroom. She is testing a new method for cleaning up ancient DNA. It's the second day of her protocol, the first time with 'real samples' instead of artificial test sequences, and it’s a very long day. The ancient DNA-snippets need to be attached to tiny magnetic beads, then washed, washed again, replicated, fitted with more adapters and more – plus the new step, the actual experiment, the attempt to remove even more of the contaminating modern DNA.
Everything is strictly by the book – and then again, of course, it is very much not.

Everything takes time. The minutes quickly add up. Ten to defrost. Fifteen of shaking here, thirty for a ride there. Washing, heating, cooling. More shaking... In the windowless room, with the constant hum of vents and freezers and the vibration of the hoods in synch with the ventilation system, one almost feels as if in the bowels of a ship, with some mighty diesel engine pounding in the rear.

Everybody in the lab is caught up in her own cycle of procedures, her own strict protocol. Coordinating common lunchbreaks becomes a logistic challenge of its own. „It’s important, though“, says Marie. „In the lab we all have to be so focused, so single-minded. Without lunch, we wouldn’t get to talk to each other all day.“

Even when your samples are on one of their rides, you rarely have a spare moment.
Tubes need to be labeled, tiny tubes, that easily slip from your gloved hands. The labels need to be printed. Everything needs to be double-checked. As with every library in the world: if you screw up the labels, the sample is essentially worthless.
Then the buffer runs out. Ice packs need to be refilled. The suckers of the centrifuge come loose. Time flies.

At the end of the day: Twenty-four tubes of DNA libraries, ready to leave the cleanroom and go upstairs (to a lab with daylight!) to be prepared for sequencing. Twenty-four more of leftovers, to be archived in the freezers. Because you can never know, if somewhen, some time, someone thinks of a new method to squeeze useful information out of them.


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