Multi-Omics Resources for Translational Medicine Research

General Omics Data Sets

• NCBI GEO: Gene Expression Omnibus
• NCBI SRA: Sequence Read Archive
• NCBI dbGaP: The database of Genotypes and Phenotypes
• NCBI dbVar: Human Structural Variant Data Hub
• EMBL-EBI EGA: European Genome-phenome Archive
• EMBL-EBI ArrayExpress: Functional Genomics Data
• BioGPS: BioGPS Dataset Library
• recount2: Analysis-Ready RNA-seq Gene and Exon Counts Datasets
• UCSC Xena Data Hubs: Normalized Public Omics Data Hubs with UCSC's own Data Sets

Disease Data Sets

• NCI Data Catalog: Data Collections Produced by Major NCI Initiatives.
• TCGA: The Cancer Genome Atlas or Broad GDAC Firehose
• ICGC: The International Cancer Genome Consortium
• CCLE: The Cancer Cell Line Encyclopedia
• cBioPortal for Cancer Genomics
• METABRIC: The Genomic Profiles of 2,509 Breast Cancers
• Broad Institute Cancer Program Datasets
• GENIE: The AACR Project Genomics, Evidence, Neoplasia, Information, Exchange
• MSK-IMPACT: Targeted Sequencing of 10,000 Metastatic Cancer Cases
• PCGP: Pediatric Cancer Genome Project
• HAS: The Hungarian Academy of Science Breast Cancer and Ovarian Cancer Data Sets
• SMRI: Stanley Medical Research Institute Brain Research Data Sets
• SFARI-SSC: Simons Simplex Collection of Autism
• PsychENCODE: The Psychiatric Disease Brain Data Sets

Reference Model Databases

• EMBL-EBI Ensembl: Reference Genome Assembly
• NHGRI GENCODE: Encyclopedia of Genes and Gene Variants
• NHGRI ENCODE: Encyclopedia of DNA Elements
• GTEx: The Genotype-Tissue Expression Project
• 1KGP: The 1000 Genomes Project
• The 1000 Genomes TagSNP Database
• IGP: The Immunological Genome Project
• HPA: The Human Protein Atlas
• ClinGen: The Clinical Genome Resource
• PGKB: The Pharmacogenomixs Knowledgebase
• CPIC: The Clinical Pharmacogenetics Implementation Consortium
• OncoKB: Precision Oncology Knowledge Base
• Allen Institute Human Brains: Bulk Transcriptomts from Healthy Human Donor Brains

Single Cell Omics Data Sets

• Broad Institute Single Cell Portal: Single Cell Transcriptomes of Oligodendroglima/Astrocytoma/Melanoma
• NYGC Satija Lab: 2,700 + 33,000 blood cells
• NYU Yanai Lab: 8,500 pancrea cells
• 10X Genomics: Single Cell Gene Expression Datasets
• JingleBells: A Repository of Standardized Single Cell RNA-Seq Datasets
• Salk Institute Human and Mouse Frontal Cortex Methylomes: Single Cell Methylomes of 3,377 and 2,784 Neurons from the Frontal Cortex of Mice and a Human
• Allen Brain Atlas: 15,928 Single Cell Transcriptomes from Four Postmortem Donor Brains and Four Neurosurgical Donor Brains
• UCSD Brain Single Cells: >60,000 Single Nucleus Transcriptomes and Single Cell DNA Accessibility Maps of Human Adult Brain Cells
• HCA: The Human Cell Atlas. The data of 30,000,000+ cells is not available yet.
• FlowRepository: Database of flow cytometry experiments

Epidemiology

• NCI SEER: Cancer Surveillance, Epidemiology, and End Result Program

Online Tools

• UCSC Genome Browser
• NCBI BLAST: Basic Local Alignment Search Tool
• Broad Institute GSEA: Gene Set Enrichment Analysis
• NCBI GDP: Genome Decoration Page

Resources

• NCBI PubMed
• NCBI Handbook
• NCBI All Resources
• OMICtools
• Bioconductor Workflows
• RNA-Seq Blog: Transcriptome Sequencing Research & Industry News
• University of Pittsburgh OBRC: Online Bioinformatics Resources Collection
• Dr. Andrew Kropinski's Internet Resources for Molecular Biologists

Acknowledgements

Thanks to Dr. Abdulkadir Elmas for providing a new item.

Please let me know if I miss something.