Integrated human endoderm-derived organoids cell atlas (HEOCA) v1.0

The datasets below are ingested in the HCA Data Portal and used in the creation of the related integrated atlas. Additional datasets may have been used in the creation of the atlas. See the atlas publication for the full list of source datasets for the atlas.

Project Title	Species	Method	Anatomical Entity	Disease (Donor)	Cell Count Est.
A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates	Homo sapiens	5 library construction methods	2 anatomical entities	normal	78,901
A Human Liver Cell Atlas reveals Heterogeneity and Epithelial Progenitors	Homo sapiens	CEL-seq2	liver	3 diseases	10,000
A human liver organoid screening platform for DILI risk prediction	--	--	--	--	--
A human multi-lineage hepatic organoid model for liver fibrosis	--	--	--	--	--
Adaptable haemodynamic endothelial cells for organogenesis and tumorigenesis	--	--	--	--	--
An integrated transcriptomic cell atlas of human endoderm-derived organoids	--	--	--	--	--
An organoid and multi-organ developmental cell atlas reveals multilineage fate specification in the human intestine	Homo sapiens	2 library construction methods	5 anatomical entities	Unspecified	Unspecified
An organoid‐derived bronchioalveolar model for SARS‐CoV‐2 infection of human alveolar type II‐like cells	--	--	--	--	--
BMP gradient along the intestinal villus axis controls zonated enterocyte and goblet cell states	--	--	--	--	--
Cholangiocyte organoids can repair bile ducts after transplantation in the human liver	--	--	--	--	--
Development of a quantitative prediction algorithm for target organ-specific similarity of human pluripotent stem cell-derived organoids and cells	--	--	--	--	--
Development of human alveolar epithelial cell models to study distal lung biology and disease	--	--	--	--	--
Differentiation of Human Intestinal Organoids with Endogenous Vascular Endothelial Cells	Homo sapiens	2 library construction methods	3 anatomical entities	Unspecified	Unspecified
Differentiation of human pluripotent stem cells into functional airway basal stem cells	--	--	--	--	--
Enteric Coronavirus Infection and Treatment Modeled With an Immunocompetent Human Intestine-On-A-Chip	--	--	--	--	--
EPIREGULIN creates a developmental niche for spatially organized human intestinal enteroids	--	--	--	--	--
Gene Regulatory Network Analysis and Engineering Directs Development and Vascularization of Multilineage Human Liver Organoids	--	--	--	--	--
Generation of functional ciliated cholangiocytes from human pluripotent stem cells	--	--	--	--	--
Generation of mesenchyme free intestinal organoids from human induced pluripotent stem cells	--	--	--	--	--
Helicobacter pylori shows tropism to gastric differentiated pit cells dependent on urea chemotaxis	--	--	--	--	--
High-Resolution mRNA and Secretome Atlas of Human Enteroendocrine Cells	--	--	--	--	--
Human alveolar progenitors generate dual lineage bronchioalveolar organoids	--	--	--	--	--
Human branching cholangiocyte organoids recapitulate functional bile duct formation	--	--	--	--	--
Human distal lung maps and lineage hierarchies reveal a bipotent progenitor	Homo sapiens	2 library construction methods	lung	Unspecified	21,700
Human Intestinal Organoids Maintain Self-Renewal Capacity and Cellular Diversity in Niche-Inspired Culture Condition	--	--	--	--	--
Identification of SARS-CoV-2 inhibitors using lung and colonic organoids	--	--	--	--	--
In Vitro and In Vivo Development of the Human Airway at Single-Cell Resolution	Homo sapiens	10x 3' v2	3 anatomical entities	Unspecified	Unspecified
Induced organoids derived from patients with ulcerative colitis recapitulate colitic reactivity	--	--	--	--	--
Long-Term Expansion of Functional Mouse and Human Hepatocytes as 3D Organoids	--	--	--	--	--
Mapping Development of the Human Intestinal Niche at Single-Cell Resolution	Homo sapiens	2 library construction methods	small intestine	Unspecified	Unspecified
Maturation of human intestinal epithelium from pluripotency in vitro	--	--	--	--	--
Modeling Steatohepatitis in Humans with Pluripotent Stem Cell-Derived Organoids	--	--	--	--	--
Multilineage communication regulates human liver bud development from pluripotency	--	--	--	--	--
Optimized human intestinal organoid model reveals interleukin-22-dependency of paneth cell formation	--	--	--	--	--
Organoid cultures of early-onset colorectal cancers reveal distinct and rare genetic profiles	--	--	--	--	--
Organoid modeling of human fetal lung alveolar development reveals mechanisms of cell fate patterning and neonatal respiratory disease	--	--	--	--	--
Progenitor identification and SARS-CoV-2 infection in human distal lung organoids	--	--	--	--	--
Salivary gland organoid culture maintains distinct glandular properties of murine and human major salivary glands	--	--	--	--	--
Self-organized stem cell-derived human lung buds with proximo-distal patterning and novel targets of SARS-CoV-2	--	--	--	--	--
Single cell analysis of Monolayer and Organoid Primary Prostate Human Epithelial Cells Derived from the same patient	--	--	--	--	--
Single cell RNA sequencing for the paired TNF-free and -treated intestinal organoids	--	--	--	--	--
Single-cell atlas of human liver development reveals pathways directing hepatic cell fates	--	--	--	--	--
Single-Cell RNA-Seq Reveals that CD9 Is a Negative Marker of Glucose-Responsive Pancreatic β-like Cells Derived from Human Pluripotent Stem Cells	--	--	--	--	--
Single-Cell Sequencing of Developing Human Gut Reveals Transcriptional Links to Childhood Crohn’s Disease	--	--	--	--	--
Single-cell-resolved differentiation of human induced pluripotent stem cells into pancreatic duct-like organoids on a microwell chip	--	--	--	--	--
Single‐cell analyses reveal SARS‐CoV‐2 interference with intrinsic immune response in the human gut	--	--	--	--	--
Single‐cell transcriptomics reveals immune response of intestinal cell types to viral infection	--	--	--	--	--
Suspension culture promotes serosal mesothelial development in human intestinal organoids	--	--	--	--	--
Systematic evaluation of colorectal cancer organoid system by single-cell RNA-Seq analysis	--	--	--	--	--
The establishment of COPD organoids to study host-pathogen interaction reveals enhanced viral fitness of SARS-CoV-2 in bronchi	--	--	--	--	--
Transplantable human thyroid organoids generated from embryonic stem cells to rescue hypothyroidism	--	--	--	--	--
Use of human tissue stem cell-derived organoid cultures to model enterohepatic circulation	--	--	--	--	--