Microarray (Gene Chip) Technology
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Microarray (Gene Chip) Technology. PART 1. Part 2. Part 3. Part 4. Features – Parallelism • Thousands of genes simultaneously – Miniaturization • Small chip size – Multiplexing • Multiple samples at the same time – Automation • Chip manufacturing • Reagents. Part 1.

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Microarray (Gene Chip) Technology

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Microarray gene chip technology

Microarray (Gene Chip) Technology


Microarray gene chip technology

PART 1

Part 2

Part 3

Part 4


Microarray gene chip technology

Features

– Parallelism

• Thousands of genes simultaneously

– Miniaturization

• Small chip size

– Multiplexing

• Multiple samples at the same time

– Automation

• Chip manufacturing

• Reagents


Microarray gene chip technology

Part 1

PART 2

Part 3

Part 4


Microarray gene chip technology

Step

Step

Step


Microarray gene chip technology

Step 2

Step 1

Step 3

Step 2

Step 3


Microarray gene chip technology

Microarray Fabrication

  • Fabrication via Printing (cDNA chip)

    • DNA sequence stuck to glass substrate

    • DNA solution pre-synthesized in the lab

  • Fabrication In Situ(Affymetrix chip)

    • Sequence “built”

    • Photolithographic techniques use light to release capping chemicals

    • 365 nm light allows 20-m resolution


Microarray gene chip technology

Fabrication via printing

cDNA chip

Fabrication In Situ: Affymetrix chip


Microarray gene chip technology

Microarray (Gene Chip) Technology


Microarray gene chip technology

Microarray Features

– Parallelism

• Thousands of genes simultaneously

– Miniaturization

• Small chip size

– Multiplexing

• Multiple samples at the same time

– Automation

• Chip manufacturing

• Reagents


Microarray gene chip technology

Afftmetrix chip


Microarray gene chip technology

cDNA chip


Microarray gene chip technology

cDNA chip


Microarray gene chip technology

Fabrication via printing

cDNA chip

Fabrication In Situ: Affymetrix chip


Microarray gene chip technology

Microarray experiment and data acquisition


Microarray gene chip technology

Poly-A

mRNA

10% Biotin-labeled Uracil

Antisense cRNA

cDNA

IVT

AAAA

Cells

L

L

L

L

L

L

Fragment (heat, Mg2+)

Labeled

fragments

Hybridize

Wash/stain

Scan

Affymetrix microarray process


Hybridization and staining

L

L

L

L

L

L

L

L

L

L

L

L

Hybridization and Staining

Biotin

Labeled cRNA

GeneChip

Hybridized Array

+

+

SAPE

Streptavidin-

phycoerythrin


The result

The Result

  • A light source scans the array, causing the dyes to fluoresce

  • The glow is picked up by a sensor and is used to determine the relative abundance of the RNA

  • This information must be processed to determine the level of activity for each expressed gene


Microarray gene chip technology

cDNA microarray experiment


Microarray gene chip technology

cDNA microarray experiment


Microarray gene chip technology

cDNA microarray experiment


Microarray gene chip technology

Part 1

Part 2

Part 3

PART 4


Microarray gene chip technology

Clustering of many genes


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