AFFYMETRIX GENECHIP ARRAY STATION Pierce Chuang, Vishu Rajamani, Jeremy Rasiah By

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 Sequence Capacity Up to bases per array Probe size8 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:

Results source:

Affymetrix GeneChip Station Architecture

Detector Architecture source:

GeneChip Array source:

GeneChip Array Cross Section

Array Manufacturing Process  2: substrates, SiO 2, Si, GaAs, or Glass.  6: Linker Molecules. Ex, Aryl Acetylene  8: Mask, for photolithographic process  10: Activated Linker Molecules

Array Manufacturing Process

 This process is repeated several times to produce longer probes.  Full length probes are usually 25 nucleotides long

Questions ?