epigenome-profilinglisted

# Build Comprehensive Epigenomic Profiles with ENCODE ## When to Use - User wants to build a comprehensive epigenomic profile for a tissue or cell type - User asks about "chromatin states", "epigenome", or "histone landscape" for a biosample - User wants to identify super-enhancers, bivalent domains, or regulatory elements - User needs to assemble a panel of histone marks, accessibility, and TF binding data - User wants to run ChromHMM segmentation on ENCODE data - User asks "what epigenomic data does ENCODE have for [tissue]?" Assemble a complete epigenomic profile for a tissue or cell type by systematically gathering histone modifications, chromatin accessibility, transcription factor binding, transcription, DNA methylation, and 3D chromatin structure data from ENCODE. Interpret the resulting profile using ChromHMM chromatin state segmentation. ## Literature Foundation | Reference | Year | Journal | DOI | Citations | Contribution | |-----------|------|---------|-----|-----------|-------------| | Roadmap Epigenomics Consortium (Kundaje et al.) | 2015 | *Nature* | [10.1038/nature14248](https://doi.org/10.1038/nature14248) | ~5,810 | 111 reference epigenomes; 5-mark core model; 15/18/25-state ChromHMM | | ENCODE Phase 3 (ENCODE Project Consortium) | 2020 | *Nature* | [10.1038/s41586-020-2493-4](https://doi.org/10.1038/s41586-020-2493-4) | ~1,656 | Registry of candidate cis-regulatory elements (cCREs) across 1,310+ experiments | | Ernst & Kellis | 2012 | *Nat Methods* | [1