4D Nucleome Data Portal

Overview

The 4D Nucleome (4DN) Data Portal is a comprehensive platform for accessing, visualizing, and analyzing nucleomics data. The portal was developed by the 4D Nucleome Network, a consortium funded by the NIH Common Fund, with the goal of understanding the principles underlying nuclear organization in space and time (the 4th dimension).

The 4DN Data Portal hosts data generated by the 4DN Network and other reference nucleomics datasets, providing researchers with access to a wealth of information about the three-dimensional organization of the genome and its relationship to gene expression and cellular function.

Data and Resources

The portal offers several types of nucleomics data:

• Hi-C and Chromatin Interaction Data: Maps of chromatin interactions that reveal the 3D organization of the genome
• Microscopy Data: Super-resolution microscopy images that visualize nuclear structures
• Chromatin Tracing Data: Specialized datasets that track the spatial arrangement of chromatin
• Other Genomic Data: Including ChIP-seq, RNA-seq, and other complementary datasets

All data on the portal follows FAIR principles (Findability, Accessibility, Interoperability, and Reusability) and is made freely available to the scientific community.

Tools and Analysis

The 4DN Data Portal includes integrated tools for data visualization and analysis:

• HiGlass: A web-based viewer for exploring and comparing genomic contact matrices
• JupyterHub: Cloud-based analysis environment with example notebooks
• Micro Meta App: A tool for standardized microscope metadata entry
• REST API: Programmatic access to the 4DN database

The portal also provides standardized bioinformatics pipelines for data processing, ensuring uniformity and reproducibility across datasets.

Data Use Guidelines

When using data from the 4DN Data Portal in publications:

1. Contact the data-generating lab to discuss possible coordinated publication
2. Cite the 4DN White Paper (doi:10.1038/nature23884) and the 4DN Data Portal Paper (doi:10.1038/s41467-022-29697-4)
3. Acknowledge the 4DN lab that generated the data

Access and Support

The 4DN Data Portal requires an account for downloading files, but accounts can be created by anyone, including those not part of the 4DN Network. Public data is also available through AWS Open Data buckets.

For questions or support, contact the Data Coordination and Integration Center (DCIC) at support@4dnucleome.org.