1. Genomics I: The Transcriptome RNA Expression Analysis Determining genomewide RNA expression levels

2. Genomic analysis of gene expression Methods capable of giving a “snapshot” of RNA expression of all genes Can be used as diagnostic profile –Example: cancer diagnosis Can show how RNA levels change during development, after exposure to stimulus, during cell cycle, etc. Provides large amounts of data Can help us start to understand how whole systems function

3. Basics of microarrays DNA attached to solid support –Glass, plastic, or nylon RNA is labeled –Usually indirectly Bound DNA is the probe –Labeled RNA is the “target”

4. Cell-cycle regulated genes Each gene is a line on the longitudinal axis Treatments in different panels Cell-cycle stages are color coded at top Vertical axis groups genes by stage in which expression peaks Brown and Botstein, 1999 Alphacdc15cdc28Elu M/G1 G1 S G2 M

5. Analysis of microarray results Inherent variability: need for repetition –Biological and technical replicates Analysis algorithms –Based on statistical models Means of generating hypotheses that need to be tested

6. RNA- seq High throughput sequencing of cDNAs from biological samples Determine abundance of mRNA by representation in sequencing reads May detect variants (alternative splicing, specific alleles, etc.)

7. The structure of 2 ’,3 ’ -dideoxynucleotides Dideoxy Sequencing- The Old Way

8. The dideoxy sequencing method Figure 20-16a

9. © 2005 Prentice Hall Inc. / A Pearson Education Company / Upper Saddle River, New Jersey 07458 Summary of chain termination sequencing

11. Comparison of NextGen Sequencing Platforms

12. Pyrosequencing I (454 Strategy) Based on production of pyrophosphate during sequencing reaction Each time polymerase adds nucleotide (dNTP) to the growing strand, pyrophosphate (PPi) is released –Amount released equal to number of nucleotides added

13. Pyrosequencing II To quantitate amount of PPi released: –ATP sulfurylase converts PPi to ATP –ATP used by enzyme luciferase to produce light from the substrate luciferin The amount of light produced is directly proportional to the amount of ATP, which is proportional to the amount of PPi released

14. Pyrosequencing III Sequential addition of each dNTP gives sequence Apyrase enzyme used to degrade dNTPs after reaction completed Sequence read from amount of light emitted as each dNTP is added Nucleotide sequence Nucleotide added

15. Transcriptome Analysis by Pyrosequencing Like SAGE in that portions of each RNA are sequenced; abundance proportional to representation in sequencing “Micro reaction chambers” formed using emulsion of oil and aqueous phases to separate clones Sequencing strategy different from standard methodology; allows analysis of thousands of clones on one slide http://www.pyrosequencing.com/DynPage.aspx?id=7454 http://www.roche-applied- science.com/publications/multimedia/genome_sequencer/amplicon_07/wbt.htm http://www.roche-applied- science.com/publications/multimedia/genome_sequencer/amplicon_07/wbt.htm

16. Illumina Solexa Strategy -YouTube animation

17. -Can generate density of 10 7 clusters/cm 2

20. SOLiD Sequencing Strategy ABI site

23. Ion Torrent Sequencing Strategy -YouTube animation-YouTube animation chemistry