University of Washington Genome Center Virtual Tour.

University of Washington Genome Center

Virtual Tour

A stormy sky over Fluke Hall on the University of Washington in Seattle.

Fluke Hall houses the University of Washington Genome Center and the Washington Technology Center.

Typical work bench at the UWGC

Human DNA the UWGC wants to sequence are inserted into plasmids, next E. coli cells are

transformed with this recombinant DNA (Transformation).

The QPix is used to array E. coli cells transformed with human DNA.

The QPix will only pick the E. coli cells that appear white (have human DNA in the plasmid) versus the blue colonies (with out human DNA).

The Qiagen Biorobot adds different solutions to the E. coli cells in a stepwise process, including an alkaline solution to break open the bacteria cell. Vacuum filtration and ethanol precipitation are used to separate cell debris, and other unwanted waste from the

plasmid DNA (with human DNA insert).

The end result is concentrated DNA, which is similar to the DNA extracted in the process of DNA spooling .

The UW Genome Center technicians use the MiniTrak to prepare automated DNA

sequencing reactions.

The MiniTrak is a 384 tipped Pipette (liquid handling robot).

Once all of the solutions for the reaction have been added to the sequencing plate, the plate is placed in a thermocycler.

25 cycles

95° C

10 seconds

Denaturation

45° C-55 ° C 10 seconds Annealing

70 °C-72 °C

60 seconds

DNA Synthesis

This is the sequencer room at the Genome Center. There are 4 ABI 3700 sequencers at the center – one of them will run

your samples.

Also in the picture is a homemade agarose gel box (MCD Box 2). The buffer in this box is cooled to 4°C by a cooler beneath

the table.

Sequencer

A look inside a 3700 sequencer.

On the left there are plates of sequencing reactions, and two pipettes. These pipettes

transfer sequencing reactions into the capillary array on the right.

Reactions

2 Pipets

Capillary Array

Laser behind Here

Another view of a capillary array.

Each of the fine threads in the array is made of glass and is hollow on the inside. During a run, each capillary

contains a gel material similar to agarose, through which DNA migrates.

Gel Image from a 3700 Sequencer Chromatograms from different lanes of the Gel Image

Good quality data, sharp peaks.

Poorer quality data, rounded peaks.

A computer program named “Phred” assigns a base call (G, C, T, or A) and a quality score to each peak.

Next, a computer program named “Phrap” tries to assembles all of the reads into one

continuous piece called a “contig”.

Once the “contig” reaches a quality of less than 1 error in 10,000 Base Pairs, then the project is “finished” and submitted to Genbank.

What do researchers do with sequence data?

They can find which out genes we have in common with other organisms, and the ones

that are unique to humans.

Approximate number of genes in different organisms.

They can compare the DNA in genes of different organisms.