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

2. Overview  Introduction to DNA/RNA  Sequencing Techniques  Affymetrix GeneChip Station  GeneChip Station Architecture  Manufacturing Process  Questions

3. Introduction to DNA/RNA

4. Introduction DNA/RNA (cont’d)

5. Genes

6. 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

7. DNA Sequencing Techniques  Sequencing By Hybridization (SBH)  Ex, target DNA sequence, AGCCTAGCTGAA Sequence Capacity Up to 300000 bases per array Probe size8 micron Average Sequence Accuracy > 99.9% Sequencing required time Less than 48 hours Affymetrix Microarray Specification

8. Affymetrix GeneChip Station

9. Assay Preparation

10. Probes

11. GeneChip Array source: http://bach2.biosci.arizona.edu/http://bach2.biosci.arizona.edu/

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

13. Affymetrix GeneChip Station Architecture

14. Detector Architecture source: http://www.affymetrix.com/http://www.affymetrix.com/

15. GeneChip Array source: http://bach2.biosci.arizona.edu/http://bach2.biosci.arizona.edu/

16. GeneChip Array Cross Section

17. 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

18. Array Manufacturing Process

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

20. Questions ?