Version: 1.0

Welcome to OrganoidDB

A comprehensive database for multi-perspective exploration of bulk and single-cell transcriptome profiles of organoids.

Organoids are three-dimensional in vitro tissue cultures that are derived from pluripotent (embryonic or induced) adult stem cells or even patient-specific tissue samples. Organoids can mimic corresponding in vivo organs. They are more promising models than two-dimensional cell lines for the study of human processes and structures, disease onset and preclinical drug development.

OrganoidDB, a comprehensive transcriptome data (microarray, bulk RNA-seq and single-cell RNA-seq) resource of human and mouse organoids. 16,218 organoid samples were collected and labeled from GEO and ArrayExpress. Other types of sample are also integrated, including primary tissues and cell lines to enable comparisons to be made with organoids. As a result, 1,011 comparison and 58 development datasets were organized, including 145 scRNA-seq datasets. The raw data were cleaned and analyzed through a standard pipeline and presented the integrated data on OrganoidDB.

The “search” section enables users to search for organoid transcriptome expression at both bulk and single-cell levels under six different modes. The “browse” section allow users to view organoid samples and datasets with corresponding organoid culture information, differential genes, enriched functions/pathways, differential cell type markers, cell clustering, marker genes when available.

New download function[2024-04-07]
Data were updated.[2022-07-18]
OrganoidDB 1.0 was released.[2022-06-17]
Organoid/Tissue Specificity

An overview of a gene expression across different organoids compared with other types of cell culture and primary tissue

general overview img

Identification of organoid/tissue specific genes across different organoid/tissues types

organoid specificity img
Organoid Development
Correlation Analysis

Identification of genes correlated with development by calculating correlation as organoid cultures develop over time

general overview img

Gene-gene correlation across organoids or tissues

organoid specificity img
Organoid Comparison

Comparison of gene expressions, pathways and cell type compositions in organoid samples to those in different sample types (e.g. tissues, cell lines, and xenografts), or from different sources or different protocols

organoid comparison img

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If you use OrganoidDB in your work, please cite our publication:

OrganoidDB: a comprehensive organoid database for the multi-perspective exploration of bulk and single-cell transcriptomic profiles of organoids. Nucleic Acids Research. 2022.