Overview
- Overview - top-level summary of the current collection.
Sources
- Generating human intestinal tissue from pluripotent stem cells in vitro - deeply ingested protocol source.
- Generation of cerebral organoids from human pluripotent stem cells - deeply ingested protocol source.
- Organoid culture systems for prostate epithelial and cancer tissue - deeply ingested protocol source.
- Tumor organoid-T-cell coculture systems - deeply ingested protocol source.
- Establishment of patient-derived cancer organoids for drug-screening applications - deeply ingested protocol source.
- Establishment of human fetal hepatocyte organoids and CRISPR-Cas9-based gene knockin and knockout in organoid cultures from human liver - deeply ingested protocol source.
- Engineering human hepato-biliary-pancreatic organoids from pluripotent stem cells - deeply ingested protocol source.
- Long-term culture, genetic manipulation and xenotransplantation of human normal and breast cancer organoids - deeply ingested protocol source.
- Generation of heart-forming organoids from human pluripotent stem cells - deeply ingested protocol source.
- Generation of proximal tubule-enhanced kidney organoids from human pluripotent stem cells - deeply ingested protocol source.
- The generation of kidney organoids by differentiation of human pluripotent cells to ureteric bud progenitor-like cells - deeply ingested protocol source.
- Generation of kidney organoids from human pluripotent stem cells - deeply ingested protocol source.
- Generation of nephron progenitor cells and kidney organoids from human pluripotent stem cells - deeply ingested protocol source.
- Culture and establishment of self-renewing human and mouse adult liver and pancreas 3D organoids and their genetic manipulation - deeply ingested protocol source.
- Generation and assembly of human brain region-specific three-dimensional cultures - deeply ingested protocol source.
- Generation and long-term culture of advanced cerebral organoids for studying later stages of neural development - deeply ingested protocol source.
- Intestinal organoid cocultures with microbes - deeply ingested protocol source.
- Controlling the polarity of human gastrointestinal organoids to investigate epithelial biology and infectious diseases - deeply ingested protocol source.
- Transplantation of intestinal organoids into a mouse model of colitis - deeply ingested protocol source.
- A distal lung organoid model to study interstitial lung disease, viral infection and human lung development - deeply ingested protocol source.
- Generation of human antral and fundic gastric organoids from pluripotent stem cells - deeply ingested protocol source.
- Generation of lung organoids from human pluripotent stem cells in vitro - deeply ingested protocol source.
- Generation and characterization of hair-bearing skin organoids from human pluripotent stem cells - deeply ingested protocol source.
- Generating human bone marrow organoids for disease modeling and drug discovery - deeply ingested protocol source.
- Generation of ‘semi-guided’ cortical organoids with complex neural oscillations - deeply ingested protocol source.
- Host circuit engagement of human cortical organoids transplanted in rodents - deeply ingested protocol source.
- Generating and characterizing human telencephalic brain organoids from stem cell-derived single neural rosettes - deeply ingested protocol source.
- Production of human blood-generating heart-forming organoids and sample preparation for advanced imaging - deeply ingested protocol source.
- CRISPR screens in human neural organoids and assembloids - deeply ingested protocol source.
- Brainstem Organoids From Human Pluripotent Stem Cells - paper source queued for ingest.
- Human iPSC-Derived Hippocampal Spheroids: An Innovative Tool for Stratifying Alzheimer Disease Patient-Specific Cellular Phenotypes and Developing Therapies - paper source queued for ingest.
- A robust protocol for the generation of human midbrain organoids - paper source queued for ingest.
- Generation of caudal-type serotonin neurons and hindbrain-fate organoids from hPSCs - paper source queued for ingest.
- Protocol for generating reproducible miniaturized controlled midbrain organoids - paper source queued for ingest.
- Generation and long-term culture of human cerebellar organoids from pluripotent stem cells - paper source queued for ingest.
Round 2 additions (2026-04-09) — gap-filling
- Human sensorimotor organoids derived from healthy and ALS stem cells form neuromuscular junctions - spinal cord / neuromuscular organoid, deep-ingested.
- Generation of blood vessel organoids from human pluripotent stem cells - vascularized organoid (Nat Protoc), deep-ingested.
- Generation of insulin-producing pancreatic β cells from multiple human stem cell lines - pancreatic islet (Nat Protoc), deep-ingested.
- Generation of inner ear organoids containing functional hair cells from human pluripotent stem cells - inner ear (Nat Biotech, Koehler), deep-ingested.
- Generation and characterization of vestibular inner ear organoids from human pluripotent stem cells - inner ear (Nat Protoc 2025), deep-ingested.
- Individual brain organoids reproducibly form cell diversity of the human cerebral cortex - brain benchmarking (Velasco 2019, Nature), deep-ingested.
- An integrated transcriptomic cell atlas of human neural organoids - cross-protocol atlas (He 2024, Nature), deep-ingested.
- Organoid single-cell genomic atlas uncovers human-specific features of brain development - developmental trajectory (Kanton 2019, Nature), deep-ingested.
Round 3 additions (2026-04-09) — brain fidelity + retinal
- Reliability of human cortical organoid generation - brain reproducibility (Yoon 2019, Nat Methods, Pasca lab), deep-ingested.
- Cell stress in cortical organoids impairs molecular subtype specification - brain fidelity counterpoint (Bhaduri 2020, Nature, Kriegstein lab), deep-ingested.
- Generation of a ciliary margin-like stem cell niche from self-organizing human retinal tissue - retinal organoid (Kuwahara 2015, Nat Comms, Sasai lab), deep-ingested.
Round 4 additions (2026-04-09) — vascular intersections + islet maturation
- Engineering of human brain organoids with a functional vascular-like system - brain+vascular (Cakir 2019, Nat Methods, Park lab), deep-ingested.
- Flow-enhanced vascularization and maturation of kidney organoids in vitro - kidney+vascular (Homan 2019, Nat Methods, Lewis lab), deep-ingested.
- Generation of complex human organoid models including vascular networks by incorporation of mesodermal progenitor cells - multi-lineage+vascular (Wörsdorfer 2019, Sci Rep), deep-ingested.
- Functional, metabolic and transcriptional maturation of human pancreatic islets derived from stem cells - SC-islet maturation (Balboa 2022, Nat Biotech), deep-ingested.
Entities
Concepts
- Self-organization and directed patterning - working synthesis page.
- Brain organoid patterning and assembloids - working synthesis page.
- Gastrointestinal and endodermal organoid systems - working synthesis page.
- Kidney organoid differentiation routes - working synthesis page.
- Cardiac and hematoendothelial organoids - working synthesis page.
- Adult stem cell and patient-derived organoid platforms - working synthesis page.
- Multi-lineage and tissue complexity - working synthesis page.
- Organoid functional assays, transplantation, and coculture - working synthesis page.
- Organoid engineering, imaging, and screening - working synthesis page.
Queries
- Brain subregion별 프로토콜 비교 - 9개 뇌 subregion 프로토콜 비교 (whole cerebral, forebrain, hippocampus, midbrain, brainstem, hindbrain, cerebellum 등).
- Brain organoid 발달정도·동기화 비교 프레임워크 - 5축 비교 프레임워크 (region, reproducibility, fidelity, temporal mapping, cross-protocol alignment) 기반 분석. Round 2-4 신규 논문 (Velasco, Yoon, Bhaduri, Kanton, He) 활용.
Syntheses
- Organoid Protocol Starter Corpus - corpus-level synthesis.