Resources

Protocols:

Mint-ChIP (low input, multiplexed ChIP-seq)

• Protocol available on protocols.io
• Citation: van Galen P, et al. A multiplexed system for quantitative comparisons of chromatin landscapes. Mol Cell. 2016.

Cursor (track visualization software)

• Citation: The ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012.

Datasets:

Can’t find or access what you need? Please email egaskell@broadinstitute.org

Consortium projects

• BLUEPRINT Epigenome
• International Human Epigenome Consortium (IHEC)
• Encyclopedia of DNA Elements (ENCODE)
• Human Body Map lincRNA
• NIH Roadmap Epigenomics Project: Browser | Table

Encode Data Utilization Workshop

Learn how to search, analyze, and visualize ENCODE data in this virtual workshop!

Lab projects

Publication	Access link
Liau BB, Sievers C, et al. Adaptive chromatin remodeling drives glioblastoma stem cell plasticity and drug tolerance. Cell Stem Cell. 2017.	GSE74557
Tirosh I, et al. Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma. Nature. 2016.	GSE70630
Drier Y, et al. An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma. Nat Genet. 2016.	GSE76465
Flavahan WA, Drier Y, et al. Insulator dysfunction and oncogene activation in IDH mutant gliomas. Nature. 2016.	GSE70991
van Galen P, et al. A multiplexed system for quantitative comparisons of chromatin landscapes. Mol Cell. 2016.	GSE74359
Ryan RJH, et al. Detection of enhancer-associated rearrangements reveals mechanisms of oncogene dysregulation in B-cell lymphoma. Cancer Discov. 2015.	GSE69558
Farh KKH, et al. Genetic and epigenetic fine mapping of causal autoimmune disease variants. Nature. 2015.	Portal
Patel AP, Tirosh I, et al. Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science. 2014.	GSE57872
Ram O, Goren A, et al. Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell. 2011.	Portal
Ernst J. et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 2011.	Portal (Broad) and Portal (MIT)
Mikkelsen TS, et al. Dissecting direct reprogramming through integrative genomic analysis. Nature. 2008.	GSE11074
Ku M, Koche RP, Rheinbay E, et al. Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains.PLoS Genet. 2008.	GSE13084
Mikkelsen TS, et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature. 2007.	GSE12241(processed data is archived here)
Goren A, Ozsolak F, Shoresh N, Ku M, et al. Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA. Nat Methods. 2010.	GSE12241(processed data is archived here)