4DN data portal

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The 4D Nucleome Network aims to understand the principles behind the three-dimensional organization of the nucleus in space and time (the 4th dimension) and the role nuclear organization plays in gene expression and cellular function. The Network utilizes existing omics and imaging technologies as well as develop new ones to generate data and create resources to enable the study of the 4D Nucleome.

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Project Assessments (97)


Assessment Metrics
Target Rubric   NIH program name is available for querying NIH project name is available for querying The institution that created this dataset is available A biological assay is present and resolvable in CFDE-specified ontology (OBI) A relevant anatomical part is present and resolvable in the UBERON Ontology A relevant disease is present and resolvable in the MONDO Ontology A relevant file type is present and resolvable in the EDAM Ontology A relevant taxonomy is present and resolvable in the NCBITaxon Ontology A relevant cell line is present and resolvable in the Cellosaurus Ontology A landing page exists and is accessible A standardized ID or accession number is used to identify the dataset. The dataset is described with metadata using a formal, broadly applicable vocabulary. Information is provided on the experimental methods used to generate the data. The dataset is hosted in an established data repository, if a relevant repository exists. The dataset can be downloaded for free from the repository. Version information is provided for the dataset. Contact information is provided for the creator(s) of the dataset. Information is provided describing how to cite the dataset. Licensing information is provided on the datasetÂ’s landing page. describes the file type Globally unique identifier Machine-readable metadata Standardized metadata Resource identifier in metadata Open, Free, Standardized Access protocol Digital resource license Metadata license
pADamID on Hap1 NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric
yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00)             yes (1.00)       yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) no (0.00) no (0.00)
DNA SPRITE on GM12878 NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric
yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00)             yes (1.00)       yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) no (0.00) no (0.00)
BLISS on HEK293 cells after multi-target Crispr NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric
yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00)             yes (1.00)       yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) no (0.00) no (0.00)
Multi-contact 3C on HeLa cells NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric
yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00)             yes (1.00)       yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) no (0.00) no (0.00)
ATAC-seq on H1-hESC (Tier 1) NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric
yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00)             yes (1.00)       yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) no (0.00) no (0.00)
Chromatin tracing of BX-C in Drosophila NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric
yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00)             yes (1.00)       yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) no (0.00) no (0.00)
iMARGI on H1 cells NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric
yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00)             yes (1.00)       yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) no (0.00) no (0.00)
ChIA-PET in GM12878 NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric
yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00)             yes (1.00)       yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) no (0.00) no (0.00)
ChIA-PET in H1-hESC NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric
yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00)             yes (1.00)       yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) no (0.00) no (0.00)
sisHi-C of early embryos in vitro NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric
yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00)             yes (1.00)       yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) no (0.00) no (0.00)
Synthetic condensation assay of tudor domain NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric
yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00)             yes (1.00)       yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) no (0.00) no (0.00)
H3K4me3 PLAC-seq on embryonic C57BL/6N mouse tissue NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric
yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00)             yes (1.00)       yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) no (0.00) no (0.00)
DNase Hi-C on tissues NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric
yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00)             yes (1.00)       yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) no (0.00) no (0.00)
ChIP-seq on Hela SMC3 and CTCF NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric
yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00)             yes (1.00)       yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) no (0.00) no (0.00)
ChromEMT NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric
yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00)             yes (1.00)       yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) no (0.00) no (0.00)
Non-enriched ChIA-Drop on GM19239 NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric
yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00)             yes (1.00)       yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) no (0.00) no (0.00)
Hi-C on sync. SCC1-AID or CTCF-AID tagged Hela NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric
yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00)             yes (1.00)       yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) no (0.00) no (0.00)
sciRNA-seq on F123 cells NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric
yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00)             yes (1.00)       yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) no (0.00) no (0.00)
GAM on mouse brain cell types NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric
yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00)             yes (1.00)       yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) no (0.00) no (0.00)
Micro-C on JM8.N4 WT The FAIRshake dataset rubric
                    yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) no (0.00) yes (1.00) yes (1.00) no (0.00)                
FOF-CT - DNA-spot/trace Core File for Chromatin tracing of chrX in IMR90 The FAIRshake dataset rubric
                    yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) no (0.00) yes (1.00) yes (1.00) no (0.00)                
FOF-CT - DNA-spot/trace Core File for Chromatin tracing of chrX in IMR90 4DN data nucleome Datafile Rubric
            yes (1.00)       yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) no (0.00) yes (1.00) yes (1.00)   yes (1.00)