Publicly Available Datasets#
Last updated May 31, 2023
Dryad : Public database for publication associated datasets
Images#
Broad Bioimage Benchmark Collection : Identification and segmentation of cells and embryos in bright field, DIC and fluorescent images : Phenotype classification of C. elegans and cells
Human Protein Atlas : Extensive collection of microscopy-based data showing tissue-level and sub-cellular labeling of proteins with antibodies.
Allen Brain Atlas : Collection of single cell sequencing and microscopy data characterizing aspects of the brain.
Image Data Resource : Public database of cellular imaging data
Reicher_PooledProteinTagging_2020 : Data published in association with the paper “Pooled protein tagging, cellular imaging and in situ sequencing for monitoring drug action in real time”
MitoCheck: : Goal is to integrate information on the cellular function of human genes while providing access to microscopy images of cellular phenotypes.
Cell Cognition : Collection of live cell movies in which cells express a fluorescent nuclear label and a fluorescent label targeting sub-cellular structures, e.g. microtubules or golgi aparatus
Yeast Resource Center : Collection of yeast expressing fluorescent tagged proteins
OpenOrganelle : FIB-SEM data of individual cells with pixel-level annotations of organelles
Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes : hiPSC-derived cardiomyocytes as a model system for studying the relationship between transcript abundance and cellular organization
Allen Institute for Cell Science : Collection of datasets published by the AICS hosted on Quilt
OpenCell : Proteome-scale measurements of human protein localization and interactions
Sequences#
Therapeutics Data Commons : A collection of datasets spanning four therapeutics areas (i.e., Target Discovery, Activity, Efficacy and Safety, and Manufacturing) and two types of biomedical products (i.e., Small-Molecule Drugs and Biologics).
For a comprehensive list of available sequence datasets, please review the list published by Anush Kundaje
immuneML : Open source ecosystem for analyzing adaptive immune receptor repertoires