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   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.
sciHi-C on F121-6 cells The FAIRshake dataset rubric
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)
RNA-DNA SPRITE on pSM33 mESCs The FAIRshake dataset rubric
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)
DNA FISH on Chr4 The FAIRshake dataset rubric
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)
DamID-seq on HCT116 cells (2018-10-22) The FAIRshake dataset rubric
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)
16-fraction Repli-seq on H1-hESC The FAIRshake dataset rubric
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)
TRIP on K562 cells The FAIRshake dataset rubric
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)
Immunofluorescence on synchronyzed HeLa cells The FAIRshake dataset rubric
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)
HiChIP-seq on NIH-3T3 cells The FAIRshake dataset rubric
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)
pADamID on Hap1 The FAIRshake dataset rubric
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)
DNA SPRITE on GM12878 The FAIRshake dataset rubric
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)
BLISS on HEK293 cells after multi-target Crispr The FAIRshake dataset rubric
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)
Multi-contact 3C on HeLa cells The FAIRshake dataset rubric
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)
ATAC-seq on H1-hESC (Tier 1) The FAIRshake dataset rubric
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)
Chromatin tracing of BX-C in Drosophila The FAIRshake dataset rubric
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)
iMARGI on H1 cells The FAIRshake dataset rubric
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)
ChIA-PET in GM12878 The FAIRshake dataset rubric
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)
ChIA-PET in H1-hESC The FAIRshake dataset rubric
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)
sisHi-C of early embryos in vitro The FAIRshake dataset rubric
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)
Synthetic condensation assay of tudor domain The FAIRshake dataset rubric
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)
H3K4me3 PLAC-seq on embryonic C57BL/6N mouse tissue The FAIRshake dataset rubric
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)
DNase Hi-C on tissues The FAIRshake dataset rubric
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)
ChIP-seq on Hela SMC3 and CTCF The FAIRshake dataset rubric
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)
ChromEMT The FAIRshake dataset rubric
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)
Non-enriched ChIA-Drop on GM19239 The FAIRshake dataset rubric
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)
Hi-C on sync. SCC1-AID or CTCF-AID tagged Hela The FAIRshake dataset rubric
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)