DNA microarray

BiologyStatistics(data analysis)

Engineering(microfluidic, microfabrication, robotic automation…)

Chemistry(surface modification)

Optics(signal detection)Electronics, physics

Research Integration

Gene Expression

Gene Discovery

Genotyping (SNPs)Drug Discovery

Diagnosis

Sequencing/resequencing

Disease Barcoding, Drug Susceptibility

Crop ImprovementBasic Research

Preparation of DNA solution for microarray

PCR amplification

PCR product purification

96-well plate

Quality control

Collections of ESTs, library clones...

DNA printing solution

384-well plate

Re-racking

Modified from http://darwin.bio.uci.edu/~faculty/wagner/array2.html

Printing of DNA microarray

Modified from http://darwin.bio.uci.edu/~faculty/wagner/array2.html

Each spot represents different gene/clone

Flowers

Leaves

AAAAAAAAAA AAAAA

AAAAA AAAAA

AAAAAAAAAA

AAAAA

AAAAAAAAAA

mRNA isolation

DNA microarray probe preparation

cDNA labeling with fluorescent dyes

Modified from http://darwin.bio.uci.edu/~faculty/wagner/array2.html

Flower

Leaf

DNA microarray hybridization

Modified from http://darwin.bio.uci.edu/~faculty/wagner/array2.html

Labeled DNA hybridizes to corresponding DNA/gene

Laser excitation

Cy5: ~650 nmCy3: ~550 nm

Image overlay

No changes

Flower up-regulated genes

Leaf up-regulated genes

Cy3 labeled cDNA from etiolated seedlingsCy5 labeled cDNA from green leaves

Arabdidopsis 11.5K microarray

Girke et al. 2000

Detection of cross hybridization

Gygi et al. 1999

Correlation between protein and mRNA levels

Plant functional genomics

Basic mechanism of plant growth and developmentBasic mechanism of plant growth and development

Application in agricultural biotechnologyApplication in agricultural biotechnology

增加農作物產量創造高營養價值之農作物創造具高適應力之農作物利用農作物作為生物反應器

DNA microarrayand beyond….

Insertion site identification from knockout population

Mahalingam and Fedoroff, PNAS (2001) 13, 7420-7425

Pollack et al. 1999

DNA copy number detection

Iyer et al. Nature (2001) 409,533-38

DNA-protein interaction

MacBeath et al. (2000) Science 289, 1760-3

Protein-protein interaction (protein microarray)