Arrays:

2. Arrays: • Narrower terms include bead arrays, bead based arrays, bioarrays, bioelectronic arrays, cDNA arrays, cell arrays, DNA arrays,  gene arrays, gene expression arrays, genome arrays,  high density oligonucleotide arrays, hybridization arrays,  microelectronic arrays, multiplex DNA hybridization arrays,  nanoarrays, oligonucleotide arrays, oligosaccharide arrays, protein arrays, solution arrays, spotted arrays,  tissue arrays, exon arrays, filter arrays, macroarrays, small molecule microarrays, suspension arrays, tiling arrays, transcript arrays. Related terms include arrayed library. See also chips, microarrays.

3. Microarray Technology? What is it??

4. The future . . . • DNA microarrays (also called DNA chips or Gene chips) are miniaturized laboratories for the study of gene expression.

5. Microarrays are small pieces of glass (or silicon or nylon) about 2 or 3 cm square, coated with DNA. • The DNA is spotted by high speed robots in a very precise pattern. The droplets of DNA (measured in pL or nL) are separated by _x_ microns.

6. The surface of the array is covered with thousands, tens of thousands, (or soon with hundreds of thousands) of spots, each spot containing a different DNA oligomer. • Each oligomer in a DNA microarray can serve as a probe to detect a unique, complementary DNA or RNA molecule.

9. Many microarray experiments have been performed with Yeast. • Why? • Genome is completely sequenced and well annotated. • Select a PCR primer pair that amplifies each ORF.

10. PCR primers for sale . . . • To our sales list we add Yeast ORF specific primers for over 6,000 ORFs! These primers have been designed to amplify, from genomic DNA, the complete coding region including the start and stop codons. For yeast this is possible as very few yeast genes contain introns.

11. GCAT Animation

12. See CSUS Microarray Data • - Finding GCAT Data on SMD

13. DNA Microarray Technique (animated- requires Flash plug-in)

15. There are two distinct way of making DNA arrays: • DNA microarrays: Also referred to as "microarrays." Non- porous solid supports, such as glass have facilitated miniaturization and fluorescencebased detection. About 10,000 cDNAs can be robotically spotted onto a microscope slide and hybridized with a double labeled probe, using protocols pioneered by Pat Brown and colleagues at Stanford.

16. Gene Chips or DNA Chips • Oligomers synthesized directly on the chips (pioneered by Affymetrix). GeneChip ® is an Affymetrix product where they have adaptedphotolithographicmasking techniques used in semiconductor manufacture to produce arrays with 400,000 distinct oligonucleotides.

17. How to build a Gene Chip • Add nucleotides one by one to the growing end of an oligonucleotide, the sequence determined by the order in which the dNTPs are added to the reaction mix.  ? • Modified dNTPs are added. dNTPs can not attach to another until they are light activated. The dNTPs are added one after another to the chip surface, and photolithography is used to direct pulses of light at individual positions in the array and determine which of the growing oligonucleotides will be extended by one unit.

18. Affymetrix – • DNA is short (25 nt) • Small variances (SNPs) can be detected • Only one Dye can be used at a time DNA Microarrays • cDNA is spotted on glass plates • cDNA is from 100nt to 2kb in length • Very efficient hybridization • Small variances (SNPs) can’t be seen

19. #1 use of Microarrays- Investigate Changes in Gene Expression. Compare cells before and after perturbation: • Nutritional • Environmental • Disease • Toxin • Different Stages of Development

20. Important ?? • This opens the possibility of identifying patterns of coregulation among genes, which, in turn, reflects underlying regulatory mechanisms and function interrelationships.

21. Microarrays are the Future of Biology • Pre-Genomic Era- Study of Individual Genes using techniques of Molecular Biology. • Genomic Era- Sequencing of entire genomes. Analytical techniques include Sequencing, Gene Finding, analysis of Sequence Homology • Post-Genomic Era- Analysis of Gene Expression. Techniques include microarray, functional annotation techniques.

22. Researchers love DNA chips; Doctors will soon love DNA chips • Researchers love DNA chips because they give a huge amount of information, fast, at low cost. • Doctors will soon learn to love them because there are many times when a doctor would like to know something about a patient's genes (such as whether the patient is likely to respond well to a certain drug). When the price comes down enough, microarrays will likely become routine tools in the doctor's office.

23. Clinical Applications? • If this research pays off, scientists and doctors will see a new, more informative face of cancer for individual tumors. That could produce tremendous gains in cancer care. • Doctors could better match patients to the best treatment. That could improve the outcome and spare patients the side effects of therapies that won't help.

24. PNAS -- article

25. Why microarrays in a bioinformatics class? • Design of chips • Quantitation of signals • Extraction of groups of genes with linked expression profiles.

26. Since the development of DNA microarray technology in the late 1990s, it has become apparent that the increase in available gene expression data will eventually parallel the growth of the sequence and structure databases.

27. 2 important topics requiring computers: Data Integration • It’s important to link the data from the array • experiment with other sequence databases • (Genbank, SwissProt, etc). • If the activity of a gene has changed, you want • to be able to view pre-existing information about • the gene in order to explain the experimental • results. • To exchange array data with other researchers, • you need some standardized format.

28. Gene Clustering Group together genes with similar patterns of expression: Clustering can be thoughtof as forming a phylogenetic tree of genes or tissues. Genes arenear each other on the "gene tree" if they show a strong correlationacross experiments, and tissues are near each other on the "tissuetree" if they have similar gene expression patterns.

29. PNAS -- Alon et al. 96 (12): 6745 • Pattern searching and gene clustering of promoter regions of Drosophila olfactory receptors

30. The End