4DN data portal
projectThe 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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View Associations View AnalyticsProject Assessments (111)
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| 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. | The structure of the repository permits efficient discovery of data and metadata by end users. | The repository uses a standardized protocol to permit access by users. | The repository provides contact information for staff to enable users with questions or suggestions to interact with repository experts. | Tools that can be used to analyze each dataset are listed on the corresponding dataset pages. | The repository maintains licenses to manage data access and use. | The repository hosts data and metadata according to a set of defined criteria to ensure that the resources provided are consistent with the intent of the repository. | The repository provides documentation for each resource to permit its complete and accurate citation. | A description of the methods used to acquire the data is provided. | Version information is provided for each resource, where available. | 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 | ||
| BLISS on HEK293 cells after multi-target Crispr | NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric |
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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) | May 30, 2023 | ||||||||||||||||||
| Multi-contact 3C on HeLa cells | NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric |
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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) | May 30, 2023 | ||||||||||||||||||
| ATAC-seq on H1-hESC (Tier 1) | NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric |
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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) | May 30, 2023 | ||||||||||||||||||
| Chromatin tracing of BX-C in Drosophila | NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric |
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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) | May 30, 2023 | ||||||||||||||||||
| iMARGI on H1 cells | NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric |
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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) | May 30, 2023 | ||||||||||||||||||
| ChIA-PET in GM12878 | NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric |
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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) | May 30, 2023 | ||||||||||||||||||
| ChIA-PET in H1-hESC | NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric |
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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) | May 30, 2023 | ||||||||||||||||||
| sisHi-C of early embryos in vitro | NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric |
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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) | May 30, 2023 | ||||||||||||||||||
| Synthetic condensation assay of tudor domain | NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric |
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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) | May 30, 2023 | ||||||||||||||||||
| H3K4me3 PLAC-seq on embryonic C57BL/6N mouse tissue | NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric |
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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) | May 30, 2023 | ||||||||||||||||||
| DNase Hi-C on tissues | NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric |
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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) | May 30, 2023 | ||||||||||||||||||
| ChIP-seq on Hela SMC3 and CTCF | NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric |
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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) | May 30, 2023 | ||||||||||||||||||
| ChromEMT | NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric |
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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) | May 30, 2023 | ||||||||||||||||||
| Non-enriched ChIA-Drop on GM19239 | NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric |
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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) | May 30, 2023 | ||||||||||||||||||
| Hi-C on sync. SCC1-AID or CTCF-AID tagged Hela | NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric |
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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) | May 30, 2023 | ||||||||||||||||||
| sciRNA-seq on F123 cells | NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric |
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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) | May 30, 2023 | ||||||||||||||||||
| GAM on mouse brain cell types | NIH Common Fund Data Ecosystem (CFDE) FAIR Rubric |
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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) | May 30, 2023 | ||||||||||||||||||
| FOF-CT - DNA-spot/trace Core File for Chromatin tracing of chrX in IMR90 | The FAIRshake dataset rubric |
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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) | Nov 8, 2023 | |||||||||||||||||||||||||||
| FOF-CT - DNA-spot/trace Core File for Chromatin tracing of chrX in IMR90 | 4DN data nucleome Datafile Rubric |
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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) | Nov 8, 2023 | ||||||||||||||||||||||||||
| Contact Matrix dataset file | 4DN data nucleome Datafile Rubric |
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no (0.00) | 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) | Jun 20, 2024 | ||||||||||||||||||||||||||
| Contact Matrix dataset file | 4DN data nucleome Datafile Rubric |
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Jun 21, 2024 | ||||||||||||||||||||||||||||||||||||
| RNA-seq on KH2 ESC | The FAIRshake dataset rubric |
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yes (1.00) | yes (1.00) | yes (1.00) | yes (1.00) | yes (1.00) | yesbut (0.75) | yes (1.00) | yes (1.00) | no (0.00) | Jun 21, 2024 | |||||||||||||||||||||||||||
| 4DN data repository | The FAIRshake repository rubric |
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yes (1.00) | yes (1.00) | yes (1.00) | yes (1.00) | nobut (0.25) | yes (1.00) | yes (1.00) | yes (1.00) | nobut (0.25) | Jun 21, 2024 | |||||||||||||||||||||||||||
| Biosource KH2 ESC | The FAIRshake dataset rubric |
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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 | |||||||||||||||||||||||||||
| Biosample for ATAC-seq in epiblast stem cells (EPISC) from mouse | The FAIRshake dataset rubric |
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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 | |||||||||||||||||||||||||||
