Organoid Research Atlas

PDF: raw/sources/he 2024 an integrated transcriptomic cell atlas.pdf Article: Nature

Brain organoid에서 프로토콜간 발달정도(maturation), 세포간 동기화(reproducibility/fidelity)를 비교하려면 어느 정도 수준의 프로토콜 세분화가 필요할까? 이전 brain subregion protocol comparison query는 region identity 축에서 9개 subregion 프로토콜을 비교했지만, maturation·동기화 축은 데이터 부족으로 답할 수 없었다 . Round 2 4에서 추가된 5편 (Velasco 2019, Yoon 2019, Bhaduri 2020, Kanton 2019, He 2024)으로 이 질문에 직접 답할 수 있게 됐다.

PDF: raw/sources/bhaduri 2020 cell stress in cortical.pdf Article: Nature

PDF: raw/sources/cakir 2019 engineering of human brain.pdf Article: Nature Methods

PDF: raw/sources/homan 2019 flow enhanced vascularization and maturation.pdf Article: Nature Methods

PDF: raw/sources/balboa 2022 functional metabolic and transcriptional.pdf Article: Nature Biotechnology

PDF: raw/sources/vandervalk 2025 generation and characterization of vestibular.pdf Article: Nature Protocols 21:391 428, Feb 2026

PDF: raw/sources/kuwahara 2015 generation of a ciliary.pdf Article: Nature Communications

PDF: raw/sources/wimmer 2019 generation of blood vessel organoids.pdf Article: Nature Protocols

PDF: raw/sources/worsdorfer 2019 generation of complex human organoid.pdf Article: Scientific Reports

PDF: raw/sources/koehler 2017 generation of inner ear organoids.pdf Article: Nature Biotechnology

PDF: raw/sources/hogrebe 2021 generation of insulin producing pancreatic.pdf Article: Nature Protocols

PDF: raw/sources/pereira 2021 human sensorimotor organoids derived.pdf Article: Nature Communications

PDF: raw/sources/velasco 2019 individual brain organoids reproducibly.pdf Article: Nature

PDF: raw/sources/kanton 2019 organoid single cell genomic atlas.pdf Article: Nature

PDF: raw/sources/yoon 2019 reliability of human cortical.pdf Article: Nature Methods

This paper is best understood as a multi lineage developmental organoid protocol for distal lung organoid differentiation and maintenance. Its main distinctive contribution in this corpus is that it positions distal lung organoids as a disease, infection, and developmental model in one workflow.

This paper is best understood as a stepwise derivation and maturation protocol for robust human midbrain organoid generation from neuroepithelial stem cells. Its main distinctive contribution in this corpus is that it derives midbrain organoids from patterned neuroepithelial stem cells with reproducible dopaminergic and glial composition.

Not all organoid workflows in this corpus are developmental hPSC differentiations. A major branch instead expands adult, fetal, or patient derived tissue into organoid platforms that are closer to donor biology and often more immediately translational. Drost 2016

Brain organoid protocols in this collection now split into broad cerebral self organization, forebrain patterning, posterior brain subregion protocols, long term maturation, transplantation, and perturbation ready neural systems. Lancaster 2014

Organoid brain subregion별 프로토콜 차이를 정리해줘. 이 corpus에 포함된 brain organoid 논문 13편(ingested 7 + raw 6)을 기반으로, 뇌 subregion별 프로토콜 핵심 차이를 정리한다.

This corpus now spans a continuum from broad cerebral organoids to explicitly patterned forebrain, brainstem, midbrain, hindbrain, hippocampal, and cerebellar protocols. Lancaster 2014

This paper is best understood as a stepwise derivation and maturation protocol for brainstem organoid generation with midbrain and hindbrain progenitors. Its main distinctive contribution in this corpus is that it builds a brainstem organoid workflow that combines midbrain and hindbrain progenitors with dopaminergic, noradrenergic, cholinergic, and neural crest linked populations.

The heart oriented papers show a progression from early heart forming organoids to more elaborate models that include vascular and hematopoietic co development plus imaging preparation. Drakhlis 2021

This paper is best understood as a functional assay extension layered onto organoid culture for polarity control for gastrointestinal and colon organoid experiments. Its main distinctive contribution in this corpus is that it re engineers epithelial polarity so apical biology becomes experimentally accessible.

This paper is best understood as an engineering, imaging, or perturbation protocol layered onto organoid culture for CRISPR screening in neural organoids and assembloids. Its main distinctive contribution in this corpus is that it turns neural organoids and assembloids into pooled CRISPR screening systems.

This paper is best understood as an engineering, imaging, or perturbation protocol layered onto organoid culture for adult liver and pancreas organoid culture and genetic manipulation. Its main distinctive contribution in this corpus is that it establishes expandable adult liver and pancreas organoids and pairs them with genetic manipulation.

This paper is best understood as a multi lineage developmental organoid protocol for multi lineage hepato biliary pancreatic organoid engineering. Its main distinctive contribution in this corpus is that it models a foregut midgut boundary by fusing anterior and posterior spheroids into a hepato biliary pancreatic organoid.

This paper is best understood as an engineering, imaging, or perturbation protocol layered onto organoid culture for liver organoid establishment plus CRISPR editing. Its main distinctive contribution in this corpus is that it combines liver organoid establishment with knockin and knockout workflows.

This paper is best understood as a primary tissue or patient derived organoid culture protocol for patient derived cancer organoids for screening. Its main distinctive contribution in this corpus is that it focuses on robust establishment of patient derived cancer organoids for downstream drug screening workflows.

The endodermal side of the corpus spans both foundational derivation and later assay engineering, from gut and gastric generation through polarity control, microbe exposure, transplantation, and multi organ boundary models. McCracken 2011

This paper is best understood as a stepwise derivation and maturation protocol for single rosette telencephalic brain organoid generation and characterization. Its main distinctive contribution in this corpus is that it starts from single neural rosettes to tighten telencephalic brain organoid generation.

This paper is best understood as a multi lineage developmental organoid protocol for bone marrow organoid generation for disease modeling and screening. Its main distinctive contribution in this corpus is that it creates a bone marrow niche model with vascular, stromal, and hematopoietic elements.

This paper is best understood as a stepwise derivation and maturation protocol for foundational intestinal organoid generation from hPSCs. Its main distinctive contribution in this corpus is that it builds a stepwise hPSC to endoderm to mid/hindgut route that turns gut spheroids into intestinal organoids.

This paper is best understood as a stepwise derivation and maturation protocol for region specific brain organoids and assembloids. Its main distinctive contribution in this corpus is that it builds dorsal and ventral forebrain spheroids and then assembles them to study migration and circuit formation.

This paper is best understood as a multi lineage developmental organoid protocol for hair bearing skin organoid generation and characterization. Its main distinctive contribution in this corpus is that it builds skin organoids with appendages and sensory features rather than a simple epithelial sheet.

This paper is best understood as a stepwise derivation and maturation protocol for advanced long term cerebral organoid culture. Its main distinctive contribution in this corpus is that it pushes cerebral organoids toward later stage neural development and longer maturation windows.

This paper is best understood as a stepwise derivation and maturation protocol for human cerebellar organoid generation and long term culture. Its main distinctive contribution in this corpus is that it uses dual SMAD plus WNT and FGF8b patterning to generate cerebellar organoids with both rhombic lip and ventricular zone progenitors and support long term Purkinje cell maturation.

This paper is best understood as a stepwise derivation and maturation protocol for caudal hindbrain organoid generation with serotonin neuron enrichment. Its main distinctive contribution in this corpus is that it patterns ventral hindbrain progenitors toward caudal serotonin neurons and adapts the system into hindbrain like organoids.

This paper is best understood as a stepwise derivation and maturation protocol for foundational cerebral organoid generation from hPSCs. Its main distinctive contribution in this corpus is that it establishes the classic unguided cerebral organoid workflow with broad regional self organization.

This paper is best understood as a multi lineage developmental organoid protocol for heart forming organoid generation from hPSCs. Its main distinctive contribution in this corpus is that it captures early cardiac morphogenesis in a structured heart forming organoid model.

This paper is best understood as a stepwise derivation and maturation protocol for gastric antral and fundic organoid generation from hPSCs. Its main distinctive contribution in this corpus is that it separates gastric differentiation into antral and fundic trajectories from pluripotent stem cells.

This paper is best understood as a stepwise derivation and maturation protocol for classic nephron rich kidney organoid protocol. Its main distinctive contribution in this corpus is that it details a widely used kidney workflow that brings multiple renal progenitor populations into the same culture.

This paper is best understood as a stepwise derivation and maturation protocol for foundational lung organoid generation from hPSCs. Its main distinctive contribution in this corpus is that it offers a baseline pluripotent stem cell route into lung organoid generation.

This paper is best understood as a stepwise derivation and maturation protocol for high efficiency nephron progenitor and kidney organoid generation. Its main distinctive contribution in this corpus is that it prioritizes high efficiency nephron progenitor generation as a cleaner entry into kidney organoid production.

This paper is best understood as a stepwise derivation and maturation protocol for kidney organoid generation with improved proximal tubules. Its main distinctive contribution in this corpus is that it optimizes kidney differentiation toward stronger proximal tubule representation.

This paper is best understood as an engineering, imaging, or perturbation protocol layered onto organoid culture for semi guided cortical organoids with electrophysiology workflows. Its main distinctive contribution in this corpus is that it positions semi guided cortical organoids as a reproducible platform for oscillations, calcium imaging, and MEA readouts.

This paper is best understood as a transplantation or host engagement protocol for cortical organoid transplantation and host circuit integration. Its main distinctive contribution in this corpus is that it uses transplantation to test whether cortical organoids engage host neural circuits in vivo.

This paper is best understood as a stepwise derivation and maturation protocol for hippocampal spheroid generation from hiPSCs for disease modeling. Its main distinctive contribution in this corpus is that it creates free floating hippocampal spheroids from human iPSCs that preserve hippocampal marker identity and support early Alzheimer related phenotype readouts.

Overview top level summary of the current collection. Generating human intestinal tissue from pluripotent stem cells in vitro deeply ingested protocol source.

This paper is best understood as a functional assay extension layered onto organoid culture for colon and intestinal organoid microbial coculture workflows. Its main distinctive contribution in this corpus is that it adds lumenal microinjection, 2D exposure, and microbial viability workflows to intestinal organoids.

Kidney protocols in this collection are less about whether organoids are possible and more about which developmental route and segment balance should be prioritized. Xia 2014

Saved manifest organoid protocols manifest.tsv. Saved spreadsheet organoid protocols papers.xlsx.

This paper is best understood as an engineering, imaging, or perturbation protocol layered onto organoid culture for breast organoid derivation, engineering, and xenotransplantation. Its main distinctive contribution in this corpus is that it extends breast organoids into long term culture, genetic manipulation, and xenotransplantation.

A major trend across this collection is the move away from simple epithelial balls toward organoids with multiple coordinated lineages, appendages, or anatomical boundary relationships. Lancaster 2014

This paper is best understood as a primary tissue or patient derived organoid culture protocol for prostate epithelial and cancer organoid establishment. Its main distinctive contribution in this corpus is that it shows how healthy and cancer prostate organoids can be expanded from primary material rather than only stem cell differentiation.

The newest protocols in this collection do not stop at making organoids. They increasingly add gene editing, pooled perturbation, viral delivery, advanced imaging, or whole mount preparation to turn organoids into higher leverage experimental systems. Hendriks 2020

Several papers in this corpus are best understood as second wave protocols: they assume an organoid already exists, then teach how to expose it to microbes, immune cells, injury models, or host tissue. Cattaneo 2019

This corpus contains 29 deeply ingested organoid protocol papers spanning baseline organ generation, regional patterning, adult and patient derived platforms, functional coculture or transplantation workflows, and newer engineering or screening layers. Generating human intestinal tissue from pluripotent stem cells in vitro

This collection contains 44 deeply ingested organoid protocol papers (29 from Round 1 + 15 from Rounds 2 4 gap filling) spanning foundational hPSC differentiation, adult and patient derived systems, multi lineage developmental models, second wave assay or perturbation workflows, cross protocol benchmarking, organ+vascular intersections, and pancreatic islet maturation. finding baseline protocols for brain, gastrointestinal, kidney, heart, lung, skin, bone marrow, and gastric organoids

This paper is best understood as an engineering, imaging, or perturbation protocol layered onto organoid culture for blood generating heart forming organoids and advanced imaging. Its main distinctive contribution in this corpus is that it extends heart forming organoids toward blood generation and pairs them with scalable clearing and imaging preparation.

This paper is best understood as a stepwise derivation and maturation protocol for miniaturized controlled midbrain organoid generation for screening workflows. Its main distinctive contribution in this corpus is that it miniaturizes midbrain organoids into controlled, necrosis limited units that are compatible with higher throughput screening.

This corpus repeatedly shows the main protocol design tradeoff in organoid work: broad self organization gives richer tissue diversity, while stronger patterning gives cleaner identity and better reproducibility. Lancaster 2014

This paper is best understood as a stepwise derivation and maturation protocol for ureteric bud progenitor like route for kidney organoid generation. Its main distinctive contribution in this corpus is that it uses a ureteric bud progenitor route and chimeric culture logic rather than a nephron only strategy.

This paper is best understood as a transplantation or host engagement protocol for intestinal organoid transplantation in colitis repair model. Its main distinctive contribution in this corpus is that it moves intestinal organoids into an in vivo repair context using a colitis model.

This paper is best understood as a functional assay extension layered onto organoid culture for tumor organoid immune coculture workflow. Its main distinctive contribution in this corpus is that it turns tumor organoids into an immune interaction assay by adding T cell coculture workflows.