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Hu Cang uses a 3D printer to create his own flow cells (below)

for use in a hacked gene sequencer. The new technology aims

to capture the spatial information of biological samples.

Inside Salk 12 |15



Next generation sequencing took off about

10 years ago, thanks to new technology that

allowed comparisons of smaller, multiple

samples. This high-throughput screening en-

ables scientists to better understand diseases

like cancer by showing what groups of genes

are overexpressing on a DNA strand. Many

areas of research, like studies in metabolism,

epigenetics and plant biology, also look to next

generation sequencing to uncover how and why

disease progresses.

“We are like the glue of the Institute,” says Ku,

director of the Next Generation Sequencing

Core. Ku came to Salk in 2013 after honing her

expertise at the Broad Institute in Cambridge,

Massachusetts. “We have a common technolo-

gy that everyone is able to use no matter what

type of organism or system they’re studying,

from fruit fly to human tissue samples.”

Nearly all of the Salk labs use the sequencing

core. One of the benefits of having it onsite and

accessible to researchers is that Ku is constant-

ly doing project consultations and advising

researchers when something looks amiss.

“At other places you might send a sample off-

site and not hear back for months,” she says.

“Here, we can troubleshoot from the beginning

and give immediate feedback.”

The core is also a knowledge platform, says

Ku, who recommends (with permission) one

researcher’s technique to another. This open

exchange makes science more efficient, adds

Ku, because researchers don’t have to waste

time or resources trying attempts that others

have already worked through. “Salk is already

really collaborative, but the cores make it more

so,” she says. “No one is forced to reinvent

the wheel.”

Aside from providing expertise and training,

Ku also works with faculty to push the bound-

aries of the technology. In one collaboration,

Ku and

Hu Cang

, assistant professor, are trying

to find a way to capture the three-dimensional

information in a cell by reverse-engineering a

common genetic sequencer and combining it

with a microscope. Their goal is to capture

the spatial information of packages of DNA

(chromatin) within a cell, the shape of which

may have many implications for disease.

“In traditional sequencing, you break apart the

cell and harvest the genetic material, but you

lose all of the spatial information about that