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The NIH Roadmap Epigenomics Program: A Community Epigenetics Resource
Lisa Helbling Chadwick, Ph.D. ([email protected])
Program Director, NIH Roadmap Epigenomics Program National Institute of Environmental Health Sciences
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Where is the data: sites with unique features
Consortium homepage http://roadmapepigenomics.org • View data on genome • protocols • standards NCBI http://ncbi.nlm.nih.gov/epigenomics http://ncbi.nlm.nih.gov/geo/roadmap/epigenomics • View data • Download data • Compare samples Human Epigenome Atlas http://epigenomeatlas.org • View data on genome or with Atlas gene browser • Download data • Tools at Genboree Workbench WashU VizHub http://vizhub.wustl.edu • Next-gen browser http://epigenomegateway.wustl.edu • UCSC visualization hub at http://genome.ucsc.edu
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http://www.roadmapepigenomics.org
Links to other sites!
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Two ways to browse: Data Table
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Two ways to browse: Visual Browser
Mouse over sites, click for table
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http://epigenomebrowser.org
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Where is the data?
Consortium homepage http://roadmapepigenomics.org • View data on genome • protocols • standards NCBI http://ncbi.nlm.nih.gov/epigenomics http://ncbi.nlm.nih.gov/geo/roadmap/epigenomics • View data • Download data • Compare samples Human Epigenome Atlas http://epigenomeatlas.org • View data on genome or with Atlas gene browser • Download data • Tools at Genboree Workbench WashU VizHub http://vizhub.wustl.edu • Next-gen browser http://epigenomegateway.wustl.edu • UCSC visualization hub at http://genome.ucsc.edu
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Hot off the presses : Roadmap data at GEO
http://www.ncbi.nlm.nih.gov/geo/roadmap/epigenomics
Data download (.bed, .wig, some SRA, .bam)
View tracks on genome viewer of your choice
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Genome-wide epigenetic data at NCBI: Epigenomics Gateway
http://www.ncbi.nlm.nih.gov/epigenomics
Tutorials Text search or browser search
Compare samples
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Use filters to narrow selection
Select samples to add to clipboard
or collection, or to view metadata
(antibody, instrument,
quality metrics, sample info)
Or view on genome
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Where is the data?
Consortium homepage http://roadmapepigenomics.org • View data on genome • protocols • standards NCBI http://ncbi.nlm.nih.gov/epigenomics http://ncbi.nlm.nih.gov/geo/roadmap/epigenomics • View data • Download data • Compare samples Human Epigenome Atlas http://epigenomeatlas.org • View data on genome or with Atlas gene browser • Download data • Tools at Genboree Workbench WashU VizHub http://vizhub.wustl.edu • Next-gen browser http://epigenomegateway.wustl.edu • UCSC visualization hub at http://genome.ucsc.edu
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The Human Epigenome Atlas
Click for data
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Click to download data, or for metadata
Click to view selected data
sets
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The Human Epigenome Atlas
Genboree workbench
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Epigenomic (and other) analysis tools for your data, our data, or both
Epigenomic analysis workshop a few times a year.
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Comparison of epigenetic profiles across specific ROIs (meDIP-seq, low CpG promoters)
Cerebellum
Blood
Cortex
Davies et al., Genome Biol 2012 Similarity matrix using Pearson correlation
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Spark: cluster analysis of genomic regions of interest
multiple data
types
clusters
specific regions
http://www.sparkinsight.org Download program, video tutorials
Neilsen et al., Genome Research 2012
View regions in UCSC browser
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Where is the data?
Consortium homepage http://roadmapepigenomics.org • View data on genome • protocols • standards NCBI http://ncbi.nlm.nih.gov/epigenomics http://ncbi.nlm.nih.gov/geo/roadmap/epigenomics • View data • Download data • Compare samples Human Epigenome Atlas http://epigenomeatlas.org • View data on genome or with Atlas gene browser • Download data • Tools at Genboree Workbench WashU VizHub http://vizhub.wustl.edu • Next-gen browser http://epigenomegateway.wustl.edu • UCSC visualization hub at http://genome.ucsc.edu
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Roadmap Epigenomics VizHub at UCSC
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A new epigenomics browser
http://epigenomegateway.wustl.edu
Tutorials!
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heatmap metadata
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Easy to rearrange
tracks
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Juxtaposition: Focus in on specific genomic features or genes
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Visualize genomic interactions
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Summary
• A community resource of epigenomic maps in a variety of primary human cells and tissues
• Data can be found at several sites, including NCBI, UCSC, and sites linked from http://roadmapepigenomics.org
Thanks to…
REMC PIs: John Stamatoyannopoulos (Washington) Brad Bernstein & Alex Meissner (Broad) Joe Costello (UCSF) (and Ting Wang, Wash U) Bing Ren (UCSD) EDACC PI: Aleks Milosavljevic (Baylor)
NIH Staff: John Satterlee (NIDA) Pat Mastin (NIEHS) Fred Tyson (NIEHS) Joni Rutter (NIDA) Kim McAllister (NIEHS) Astrid Haugen (NIEHS)