Wednesday, August 10, 2011


Whole genome amplification is a very powerful technique.  With a really major caveat. 

It's blind.

It will make tons of copies of any DNA available.  Your microbe's DNA, your DNA, your dust mites' DNA, your cat's dinner's DNA.  If even a trace of DNA ends up in your reaction, it gets amplified right along with your sample.  This is called contamination.

The more limiting your sample, the bigger a problem contamination.  So if you're sequencing DNA from ancient humans, you probably only have traces amounts of ancient DNA around and lots of contaminating present day human DNA.

What's the solution to dealing with contamination?  Be really, really, clean.  In fact, use a clean room.

A clean room is a room that is sealed off and is fed filtered air.  Clean rooms are classified by how many of how small particles are let into the room.  The clean room in my lab is class 1000, which means that a maximum of 1000 particles per cubic foot of size greater than 0.5 micrometers are allowed in. 

All of this seems reasonable until you consider that a person needs to be able to enter and work in the clean room.  Obviously, a person is constantly shedding hair, skin, and DNA.

To solve this problem, we suit up and then shower down!

All ready for the clean room
Here's the get-up we wear to enter the clean room.  The suit itself is stored in a UV cabinet.  Why UV?  Because UV kills DNA.  Baking everything in UV is an easy way to eliminate contaminating DNA.

After getting all dressed up, you enter the first door to the clean room.  Inside is a small area that showers you with air.  The point is blow away contamination.  Finally, you go through a second door and are finally inside the clean room!

A trip to the old part of Tokyo, Asakusa!

Kaminarimon, Asakusa

Sensō-ji, Asakusa

Sensō-ji, Asakusa


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