507a Gene Discovery

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507a Gene Discovery

  1. 1. Into the lab DEG, SSH, degenerative PCR Lecture FISH 507a Bioinformatics
  2. 2. Stuff • Homolog Project • Query Files • question: movies • extra credit 2
  3. 3. Taking the molecular approach • evolution – comparing sequences, markers • physiological differences – comparing phenotypes • differences in expression level – first have to find the genes 3
  4. 4. How do you find genes 4
  5. 5. How do you find genes • Entrez (qualifers) • Sequence similarity (BLAST) • Large scale BLAST on ESTs • Degenerative PCR • SSH, DEG • Sequencing (can include SSH etc) 5
  6. 6. Top down approaches to Gene Discovery Differential Display and Suppression Subtraction Useful for characterizing transcriptome differences in different treatments, tissues, stages of development when there is limited genomic information or a desire to use a non-hypothesis gene target model. As opposed to…..
  7. 7. Gene discovery using a degenerative PCR Approach. 7
  8. 8. Degenerative PCR Approach
  9. 9. Basing Primers on Amino Acids 9
  10. 10. Basing Primers on Amino Acids 10
  11. 11. Examples of when you might want to compare transcriptome differences…….
  12. 12. vs Genes involved in memory
  13. 13. Growth
  14. 14. vs Environmental Effects and Virulence
  15. 15. vs Kin Recognition
  16. 16. TOP DOWN Differential Display Random Primer approach to identify genetic differences Text
  17. 17. Differential Display
  18. 18. Bay Scallop Development
  19. 19. QPX
  20. 20. Suppression-subtraction
  21. 21. Subtract / Hybridize
  22. 22. Subtract / Hybridize
  23. 23. Subtract / Hybridize
  24. 24. BONUS SLIDE
  25. 25. Sequencing • Simple cDNA library • SAGE • SSH Library 35
  26. 26. A little about new sequencing • Not necessarily new way to find genes • Though cheaper and faster – 454 – Solid state (Illumina, ABI) 36
  27. 27. DISCUSSION OF PAPER
  28. 28. RECAP 42

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