Databases and Data Portals

4D Nucleome Data Portal

Hi-C, ChIA-PET, imaging, and other nuclear organization datasets from the NIH 4DN program.

Open resource

ENCODE Project

Reference ChIP-seq, ATAC-seq, RNA-seq, and functional genomics data across many biosamples.

Open resource

Roadmap Epigenomics

Reference epigenomes across human tissues, including histone modification maps.

Open resource

Gene Expression Omnibus

Large public repository for high-throughput sequencing and microarray studies.

Open resource

ArrayExpress

EBI repository for functional genomics datasets and metadata.

Open resource

JASPAR

Curated transcription factor binding profiles.

Open resource

Ensembl

Reference genome browser with genes, variants, comparative genomics, and regulatory features.

Open resource

UCSC Genome Browser

Highly configurable genome browser with a broad track-hub ecosystem.

Open resource

AlphaFold Database

Predicted protein structures, useful for nuclear proteins and intrinsically disordered region context.

Open resource

RCSB Protein Data Bank

Experimentally determined structures, including nucleosomes, pores, and large nuclear assemblies.

Open resource

UniProt

Curated protein function, sequence features, PTMs, and interaction annotations.

Open resource

PhosphoSitePlus

Curated phosphorylation, acetylation, ubiquitination, and other PTM evidence.

Open resource

BioGRID

Protein-protein and genetic interaction records, including nuclear interactomes.

Open resource

STRING

Functional association networks with confidence scoring and enrichment tools.

Open resource

OMIM

Genetic disease entries for laminopathies, chromatinopathies, and other nuclear disorders.

Open resource

ClinVar

Clinical variant interpretations for disease-linked nuclear genes.

Open resource

cBioPortal

Cancer genomics queries across TCGA and related datasets.

Open resource

GTEx Portal

Tissue expression and eQTL context for nuclear genes.

Open resource

OpenOrganelle / CellMap

FIB-SEM whole-cell datasets with nuclear ultrastructure.

Open resource

BioImage Archive

Public biological imaging repository with study metadata.

Open resource

Image Data Resource

Published microscopy datasets that can be searched by phenotype and organism.

Open resource

CELL-IDR

High-content imaging screen datasets with nuclear phenotype use cases.

Open resource