AFFYMETRIX GENECHIP ARRAY STATION By Pierce Chuang Vishu

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

Overview Introduction to DNA/RNA Sequencing Techniques Affymetrix Gene. Chip Station Architecture Manufacturing Process Questions

Introduction to DNA/RNA

Introduction DNA/RNA (cont’d)

Genes

DNA Sequencing Techniques Chain-terminator method (Sanger) Dideoxynuclotides triphosphates (dd. NTPs) 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 Affymetrix Microarray Specification Sequence Capacity Probe size Up to 300000 bases per array 8 micron Average Sequence > 99. 9% Accuracy Sequencing required Less than 48 hours time

Affymetrix Gene. Chip Station

Assay Preparation

Probes

Gene. Chip Array source: http: //bach 2. biosci. arizona. edu/azccmicroarray/help. php 3

Results source: http: //www. med. upenn. edu/microarr/a rray. html

Affymetrix Gene. Chip Station Architecture

Detector Architecture source: http: //www. affymetrix. com/corporate/media/genechip_ essentials/gene_expression/Features_and_probes. aff x

Gene. Chip Array source: http: //bach 2. biosci. arizona. edu/azccmicroarray/help. php 3

Gene. Chip Array Cross Section

Array Manufacturing Process 2: substrates, Si. O 2, Si, Ga. As, 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 ?