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Navigable Slide Index

1. Intro slide
2. The target gene problem (1)
3. Example 1: the E2F family of transcription factors
4. Example 2: the zinc finger transcription factors
5. The target gene problem (2)
6. Do all family members regulate the same genes?
7. How can we find target genes?
8. Standard assays to identify target genes
9. The ChIP assay
10. Controls for ChIP assays
11. Identification of in-vivo binding sites
12. Cloning/sequence analysis of ChIP fragments
13. PCR amplification of candidate promoters
14. How can one identify candidate target promoters?
15. Combining gene expression profiling and ChIP
16. Targets may be missed due to primer location
17. Analyzing ChIP samples using microarrays
18. ChIP-on-chip analyses (1)
19. Amplicon verification
20. ChIP-on-chip analyses (2)
21. Types of Microarray Platforms
22. ChIP-on-chip analyses (3)
23. Analysis of candidate promoters
24. High throughput analysis of candidate promoters
25. Analysis of genomic tiling array (1)
26. Combining microarray analyses
27. What is a CpG microarray?
28. How do you obtain CpG islands?
29. Creation of a CpG island library
30. Experimental design for ChIP-CpG
31. How do you analyze CpG arrays?
32. Identification of positive CpG islands
33. Experimental design
34. Analysis of genomic tiling arrays (2)
35. ChIP-on-chip analyses: promoter arrays
36. Core promoter arrays
37. Tiled core promoter arrays
38. ChIP-on-chip analyses: whole genome arrays
39. Genomic tiling arrays: screening an entire genome
40. Example of mapping E2F1 binding sites
41. Experimentally determined/consensus sites
42. Some consensus E2F sites are bound by E2F1
43. The location of the E2F site determines occupancy
44. Confirmation steps
45. Confirmation using amplicons
46. Confirmation using a biological replicate
47. Have you identified a bona fide target gene?
48. Does factor binding regulate the target gene?
49. E2F6 siRNA
50. E2F6 knockdown affects gene expression
51. Summary
52. Advantages of ChIP-on-chip
53. Limitations of the current technology
54. Websites for detailed protocols

Topics Covered

• Identifying genomic targets of DNA-binding factors
• Experimental methods
• Chromatin immunoprecipitation (ChIP) assay
• Probing microarrays
• ChIP-on-chip assays for comprehensive analysis
• Data interpretation and follow-up studies

Links

Series:

• Eukaryotic Gene Regulation

Categories:

• Cell Biology
• Genetics & Epigenetics
• Methods

Talk Citation

Publication History

• Published on October 1, 2007
• Archived on July 13, 2015

Financial Disclosures

• Prof. Peggy Farnham has not informed HSTalks of any commercial/financial relationship that it is appropriate to disclose.