EpiATLAS - a reference for human epigenomic research
The International Human Epigenome Consortium (IHEC) has led a global effort to compile and uniformly process the most extensive collection of human epigenomes to date, representing healthy and diseased cells and tissues from 2,897 individuals. This initiative builds on primary data generated by multinational consortia and has been supported by the development of standardized bioinformatics protocols, data models, and analysis tools to manage and interpret large-scale epigenomic data. Central to this work is the creation of the Epigenome Reference Registry—a publicly accessible resource that enables open searching of de-identified samples and experimental data, while providing a framework for secure access to protected datasets. Together, these efforts support a robust, integrated ecosystem for human epigenome research, advancing our understanding of cell- and tissue-specific regulatory landscapes.
Download the Data
The EpiATLAS dataset is the result of a multi-year effort to collect, curate, and uniformly process human epigenomic data from 10 international IHEC projects. Data access applications were submitted to major repositories including EGA, dbGaP, and NBDC, with approvals and data acquisition spanning over four years. Once acquired, all data and metadata were reviewed, curated, and organized by Canada’s Michael Smith Genome Sciences Centre to support centralized analysis. This resource includes 7,494 uniformly processed analysis objects across RNA-seq, whole genome bisulfite sequencing (WGBS), and ChIP-seq, representing 337 complete and 2,022 partial epigenomes. The final dataset includes 28.8TB of raw data and an additional 6TB of processed data, all available for download below.
Terms & Conditions
The downloading of this data is subject to monitoring. By using this data, you acknowledge that you are using the data for health research purposes and will not attempt to re-identify research participants. Should you come across any directly or indirectly identifying data, you agree to report it quickly to info@ihec-epigenomes.org
Acknowledgements
If you used the IHEC reprocessed and harmonized data in your paper, also known as the EpiATLAS dataset, you should include in the acknowledgements:
“We thank the International Human Epigenome Consortium (IHEC) for providing access to reprocessed and harmonized epigenomic data from a broad collection of human cell types.” You should also cite the main EpiATLAS paper, see below.
How do I cite the main EpiATLAS paper?
Please cite: “International Human Epigenome Consortium, EpiATLAS - a reference for human epigenomic research, in preparation.”
EpiATLAS Resources
We have assembled a collection of resources—including standardized metadata, processing pipelines, and visualization tools—to support users in navigating and interpreting the EpiATLAS data.
The EpiATLAS Standardized Analysis Pipelines GitHub repository hosts reproducible workflows for processing RNA-seq, WGBS, and ChIP-seq data, enabling consistent and high-quality analysis across the EpiATLAS dataset.
The EpiATLAS Standardized Analysis Pipelines GitHub repository hosts reproducible workflows for processing RNA-seq, WGBS, and ChIP-seq data, enabling consistent and high-quality analysis across the EpiATLAS dataset.
epilogos provides summarized views of large amounts of genome-wide datasets. The epilogos Search tool discovers chromatin state logos — epilogos — in your genomic intervals.
This IHEC Data Portal can be used to view, search and download the data already released by the different IHEC-associated projects.
epilogos provides summarized views of large amounts of genome-wide datasets. The epilogos Search tool discovers chromatin state logos — epilogos — in your genomic intervals.
The IHEC bioRxiv channel showcases the research publications from the International Human Epigenome Consortium, highlighting advances in epigenomic data generation, analysis, and applications in health and disease.