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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 (111)


Assessment Metrics Date
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 A1.1 Access Protocol A1.2 Access Authorization A2 - Metadata Longevity 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 F1.A Identifier Uniqueness F1.B Identifier persistence F2. Machine-readability of metadata F3. Resource Identifier in Metadata Globally unique identifier Machine-readable metadata Standardized metadata Resource identifier in metadata F4. Indexed in a searchable resource Open, Free, Standardized Access protocol Digital resource license Metadata license
ATAC-seq on KH2 ESC 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) Jun 21, 2024
RNA FISH in mouse embryonic stem cells ES-E14TG2a 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) Jun 21, 2024
Biosource KH2 ESC The FAIRshake dataset rubric
                          yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) nobut (0.25) yes (1.00) yes (1.00) nobut (0.25)                           Jun 21, 2024
4DN Jupyter Hub Tool - BETA FAIR_test
                    yes (1.00) no (0.00) yes (1.00)                     no (0.00) no (0.00) yes (1.00) yes (1.00)         yes (1.00)       Aug 27, 2024
multiplexed FISH on IMR-90 The FAIRshake dataset rubric
                          yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) nobut (0.25) yes (1.00) yes (1.00) nobut (0.25)                           Dec 11, 2024
multiplexed FISH on IMR-90 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) yes (1.00) yes (1.00) Dec 11, 2024
single cell RNA-seq on primary motor cortex from mouse - subsection 5D - Biological Replicate 1 The FAIRshake dataset rubric
                          yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) nobut (0.25) yes (1.00) yes (1.00) nobut (0.25)                           Dec 12, 2024
single cell RNA-seq on primary motor cortex from mouse - subsection 5D - Biological Replicate 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) yes (1.00) yes (1.00) Dec 12, 2024
HCT116 Human colon carcinoma cell line 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) yes (1.00) yes (1.00) Dec 12, 2024
HCT116 Human colon carcinoma cell line The FAIRshake dataset rubric
                          yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) nobut (0.25) yes (1.00) yes (1.00) nobut (0.25)                           Dec 12, 2024
Contact matrix mcool file output file of the Hi-C processing pipeline 4DN data nucleome Datafile Rubric
            nobut (0.25)             yes (1.00) yes (1.00) yes (1.00) yes (1.00) yes (1.00) nobut (0.25) yes (1.00) yes (1.00)   yes (1.00)                         Dec 12, 2024