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Printable Handouts
Navigable Slide Index
- Introduction
- The human genome
- The ENCODE project
- Accessing and using ENCODE data
- Advantages of studying genome in a consortium
- ChIP-seq guidelines
- ENCODE assays
- ENCODE assay: RNA-seq
- ENCODE assay: ChIP-seq
- Evolution of the ChIP assay
- ENCODE assays: regulatory chromatin
- ChIP-seq of modified histones
- Open chromatin and TF binding sites
- ENCODE assays: 3D looping
- What has been learned so far
- An integrated encyclopedia of DNA elements
- Insights from ENCODE
- Density of information encoded in human genome
- Protein-coding transcripts
- Comparison of coding and non-coding RNAs
- Open chromatin
- Chromatin modifications that influence expression
- Classification of transcription factors
- Transcription factor binding preferences
- Chromosomal loops
- ENCODE elements are linked to genetic variation
- The ENCODE explorer
- How to access ENCODE data
- Visualizing ENCODE data
- ENCODE data on the UCSC genome browser
- Integrated ENCODE regulation tracks
- Snapshot of ENCODE tracks
- Expression and regulation ENCODE tracks
- How to access tables listing ENCODE data
- ENCODE experiment matrix
- ENCODE experiment summary
- Downloading ENCODE data
- ENCODE resources
- ENCODE user’s guide
- Using ENCODE data
- Understanding ChIP-seq results
- ENCODE standards for ChIP-seq
- Reproducibility and peak-cut off
- Comparing a ChIP-seq peak file to other datasets
- Tag density plots of ChIP-seq data
- Analysis of target genes
- Motif analysis: Factorbook
- Example from Factorbook
- ZBTB33 sequence logos
- Understanding GWAS results
- The genomic landscape around a risk SNP
- Tag SNPs and functional SNPs
- FunciSNP
- Example of FunciSNP workflow
- Identification of functional SNPs
- 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:
Talk Citation
Farnham, P. (2013, November 5). Accessing and using ENCODE data [Video file]. In The Biomedical & Life Sciences Collection, Henry Stewart Talks. Retrieved April 18, 2021, from https://hstalks.com/bs/2679/.Publication History
Financial Disclosures
- Prof. Peggy Farnham has not informed HSTalks of any commercial/financial relationship that it is appropriate to disclose.