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 ?
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