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1. Introduction
2. The human genome
3. The ENCODE project
4. Accessing and using ENCODE data
5. Advantages of studying genome in a consortium
6. ChIP-seq guidelines
7. ENCODE assays
8. ENCODE assay: RNA-seq
9. ENCODE assay: ChIP-seq
10. Evolution of the ChIP assay
11. ENCODE assays: regulatory chromatin
12. ChIP-seq of modified histones
13. Open chromatin and TF binding sites
14. ENCODE assays: 3D looping
15. What has been learned so far
16. An integrated encyclopedia of DNA elements
17. Insights from ENCODE
18. Density of information encoded in human genome
19. Protein-coding transcripts
20. Comparison of coding and non-coding RNAs
21. Open chromatin
22. Chromatin modifications that influence expression
23. Classification of transcription factors
24. Transcription factor binding preferences
25. Chromosomal loops
26. ENCODE elements are linked to genetic variation
27. The ENCODE explorer
28. How to access ENCODE data
29. Visualizing ENCODE data
30. ENCODE data on the UCSC genome browser
31. Integrated ENCODE regulation tracks
32. Snapshot of ENCODE tracks
33. Expression and regulation ENCODE tracks
34. How to access tables listing ENCODE data
35. ENCODE experiment matrix
36. ENCODE experiment summary
37. Downloading ENCODE data
38. ENCODE resources
39. ENCODE user’s guide
40. Using ENCODE data
41. Understanding ChIP-seq results
42. ENCODE standards for ChIP-seq
43. Reproducibility and peak-cut off
44. Comparing a ChIP-seq peak file to other datasets
45. Tag density plots of ChIP-seq data
46. Analysis of target genes
47. Motif analysis: Factorbook
48. Example from Factorbook
49. ZBTB33 sequence logos
50. Understanding GWAS results
51. The genomic landscape around a risk SNP
52. Tag SNPs and functional SNPs
53. FunciSNP
54. Example of FunciSNP workflow
55. Identification of functional SNPs
56. Summary

Topics Covered

• A description of the ENCODE Consortium
• Experimental assays used by Consortium members
• Overview of genome-wide methods to study gene expression, chromatin, and transcription factors
• A summary of insights from ENCODE experiments
• How to access and download ENCODE data
• How to use ENCODE data in your own research

Links

Series:

• Epigenetics, Chromatin, Transcription and Cancer
• Eukaryotic Gene Regulation
• Introduction to Human Genetics
• Using Bioinformatics in the Exploration of Genetic Diversity

Categories:

• Biochemistry
• Cell Biology
• Genetics & Epigenetics
• Methods
• Omics & Systems Biology

Talk Citation

Publication History

• Published on November 5, 2013
• Reviewed on November 5, 2014