OrganoidDB

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.