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Molecular Biology

Molecular Biology. Dr. Chaim Wachtel April 4, 2013. GENE EXPRESSION. Topics. Microarray Deep Sequencing PCR Real-Time Digital Nanostring. Microarray. Affymetrix Agilent Same idea different implementation Pros and cons to each method. The Chips. Agilent. Affymetrix.

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Molecular Biology

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  1. Molecular Biology Dr. ChaimWachtel April 4, 2013

  2. GENE EXPRESSION Topics • Microarray • Deep Sequencing • PCR • Real-Time • Digital • Nanostring

  3. Microarray • Affymetrix • Agilent • Same idea different implementation • Pros and cons to each method

  4. The Chips Agilent Affymetrix

  5. Printing of Affymetrix Chips

  6. Printing of Agilent Chips

  7. Printing of Agilent Chips Probes are 60 nucleotides in length vs 25 for Affymetrix

  8. Affymetrix workflow

  9. Agilent workflow

  10. Analysis “home-made”=low-density • Feature Extraction • Bioinformatics Agilent array

  11. Pros and Cons • Cost • Dual color vs single • Specificity

  12. Deep Sequencing Next Generation Sequencing (NGS)

  13. Sanger Sequencing

  14. Multiple Platforms • Illumina • 454 • Solid • Nanopore/Oxford • Ion Torrent

  15. Different companies different methods

  16. Workflow for Sequencing

  17. Workflow for Sequencing • Depends on project- RNA or DNA • Protocols are ~90% the same for all systems

  18. Illumina

  19. Workflow for Sequencing • Bridge PCR • Emulsion PCR

  20. Sequencing with Illumina

  21. Sequencing with Solid

  22. The Ion Torrent

  23. Scalability

  24. The Chip

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