4D Nucleome Data Portal
A platform to search, visualize, and download nucleomics data.

Introduction

The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets, and an expanding tool set for open data processing and visualization.

The 4D Nucleome Network aims to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development as well as various diseases. The program is developing novel tools to explore the dynamic nuclear architecture and its role in gene expression programs, models to examine the relationship between nuclear organization and function, and reference maps of nuclear architecture in a variety of cells and tissues as a community resource.

Click Browse to see the available data. If you are a Network member, please log in to access internally released preliminary data sets. Please direct any questions on the data portal to the Data Coordination and Intregration Center.

Data Use Guidelines

The data at the 4DN Data Portal is generated by the 4DN Network and made freely available to the scientific community.

  • For unpublished data that you are intending to use for a publication, we ask that you please contact the data generating lab to discuss possible coordinated publication. In your manuscript, please cite the 4DN White Paper (doi:10.1038/nature23884), and please acknowledge the 4DN lab which generated the data.
  • For published data please cite the relevant publication.

Please direct any questions to the Data Coordination and Intregration Center.

Announcements

September 2018 Public Data Release Updates

Since our last data release updates in June, 110 Experiment Sets generated by 4DN have been released to the public, including the portal's first single cell Hi-C, MARGI, and Single Particle Tracking (SPT) experiment sets. Details can be found here.

HiC Processing Pipeline is in production!
The 4DN HiC processing pipeline has finished running on released HiC data sets. Experiment sets that have been analyzed with our pipeline can be found here. Resulting processed files include contact lists (pairs file) as well as contact matrices (hic and mcool files), and the mcool contact matrix is displayed in a HiGlass browser to the left of the processed file listing on each experiment set page. Clicking on the ‘Graph’ tab will display a provenance graph of files generated with the HiC pipeline.

Our pipelines are packaged open source using Common Workflow Language (CWL) and Docker containers, which can be found on GitHub. They are executed openly on the cloud environment using our home-grown cloud resource management system Tibanna.
June 2018 Public Data Release Updates

Between our first data freeze in mid-February 2018 and June 1, 2018, we are pleased to announce the public release of 78 new experiment sets on the data portal. See the Public Release Updates page for details.

HiGlass is Here!

We have recently integrated a HiGlass browser for visualization of HiC results. To use HiGlass in the portal, click on a HiC experiment set (such as 4DNES2M5JIGV), then in the processed files tab and click on an mcool file. The page for each mcool file will have a HiGlass browser tab. Some instructions on using HiGlass can be found here.

First Data Freeze and Public Release Updates
Our first data freeze is in effect. So far this year a total of 59 new experiment sets have been released to the public and included in the current freeze. See the Public Release Updates, or browse the Experiment Sets.
The 4D Nucleome Perspective is Published
The 4D Nucleome Project perspective paper is online in Nature today. If you use any 4DN data, please cite this paper. A more extensive data release and use policy will be available soon.
Reference Repli-seq Data Released
Part of the goals of 4DN involves generating reference data sets for selected cell types to study how different experiment types complement each other in our understanding of nucleome dynamics. Today, 4DN released reference Repli-seq data for the selected Tiered cell lines.
First 4DN Experiments Released
The first 4DN Funded Hi-C experiments have been released to public on the portal.
Ontology Utilization Updated
Ontology Terms from OBI, Uberon, and EFO are now represented on our database. Ontology terms can be internally used to describe cell lines and tissues. We will implement ontology utilization for other appropriate fields in the coming months.
Data Submission Open (Beta)
The 4DN Data Portal is open for beta-testers for data submission for Hi-C and related experiments.