AFFYMETRIX GENECHIP ARRAY STATION

Pierce Chuang, Vishu Rajamani, Jeremy RasiahBy

Overview

Introduction to DNA/RNA Sequencing Techniques Affymetrix GeneChip Station GeneChip Station Architecture Manufacturing Process Questions

Introduction to DNA/RNA

Introduction DNA/RNA (cont’d)

Genes

DNA Sequencing Techniques Chain-terminator method (Sanger)

Dideoxynuclotides triphosphates (ddNTPs) as DNA chain terminators

Sequence roughly 550,000 bases in a day Requires thirty years of uninterrupted

operation to sequence all nucleotides in the human genome

DNA Sequencing Techniques Sequencing By Hybridization (SBH)

Ex, target DNA sequence, AGCCTAGCTGAA

TTTCGGATCGAC

ATCGACTT

GATCGACT

GGATCGAC

CGGATCGA

TCGGATCGSequence Capacity Up to 300000 bases per

arrayProbe size 8 micron

Average Sequence Accuracy

> 99.9%

Sequencing required time

Less than 48 hours

Affymetrix Microarray Specification

Affymetrix GeneChip Station

Assay Preparation

Probes

GeneChip Array

source: http://bach2.biosci.arizona.edu/

Results

source: http://www.med.upenn.edu/

Affymetrix GeneChip Station Architecture

Detector Architecture

source: http://www.affymetrix.com/

GeneChip Array

source: http://bach2.biosci.arizona.edu/

GeneChip Array Cross Section

Array Manufacturing Process

2: substrates, SiO2, Si, GaAs, or Glass. 6: Linker Molecules. Ex, Aryl Acetylene 8: Mask, for photolithographic process 10: Activated Linker Molecules

Array Manufacturing Process

Array Manufacturing Process

This process is repeated several times to produce longer probes.

Full length probes are usually 25 nucleotides long

Questions ?