WORC Community | Protocols for NAM Models

WORC Community • Living protocols table

Highlighted Protocols for NAM Models

Selected protocols and protocol-focused literature for Organoid, Organ-on-a-Chip and Assembloid models. Protocol discovery focused on Nature Protocols and STAR Protocols. 1 January 2023 to present.

Protocols & workflows: 86

Protocol Sources

Direct searches for Organoid and Organ-on-a-Chip protocols

Nature Protocols • Organoids

Source: Nature

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Nature Protocols • Organ-on-a-Chip

Source: Nature

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STAR Protocols • Organoids

Source: Cell Press

Journal: STAR Protocols

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STAR Protocols • Organ-on-a-Chip

Source: Cell Press

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Highlighted Protocols

67 verified protocol & workflow links • 5 shown at a time

Qkine

Growth Factors and Cytokines for Organoid Research

Organoid culture resource covering animal-origin-free growth factors and cytokines for intestinal, cardiac, lung, breast, liver, brain and other organoid models, with guidance aimed at improving reproducibility and scale-up.

View resource ↗

STEMCELL Technologies

Generate Human Intestinal Organoid-Derived Monolayers

Protocol for intestinal organoid-derived monolayers and optional air-liquid interface differentiation.

#	Protocol / Workflow / Resource	Source / Provider	NAM Model / Technology	Protocol / Workflow Focus	Protocol / Resource Link
1	Organoid Culture Guide	ATCC	Organoid	Organoid culture setup, expansion and cryopreservation.	View protocol ↗
2	Generate Human Intestinal Organoid-Derived Monolayers	STEMCELL Technologies	Organoid	Protocol for intestinal organoid-derived monolayers and optional air-liquid interface differentiation.	View protocol ↗
3	Organoid & 3D Culture Protocol Resources	R&D Systems / Bio-Techne	Organoid	Protocol resources for intestinal, lung and brain organoid culture.	View protocol ↗
4	Culture and analysis of kidney tubuloids and perfused tubuloid cells-on-a-chip	Nature Protocols	Organ-on-a-Chip / MPS	Kidney tubuloid culture plus perfused microfluidic organ-on-chip workflow.	View protocol ↗
5	Long-term culture, genetic manipulation and xenotransplantation of human normal and breast cancer organoids	Nature Protocols	Organoid	Breast and breast-cancer organoid derivation, long-term culture and manipulation.	View protocol ↗
6	Culture and establishment of self-renewing human and mouse adult liver and pancreas 3D organoids	Nature Protocols	Organoid	Liver and pancreas organoid culture and genetic manipulation.	View protocol ↗
7	Microfabrication of human organs-on-chips	Nature Protocols	3D NAM / workflow	Fabrication workflow for microengineered human organ-chip systems.	View protocol ↗
8	Generating and analyzing organ-on-chip using human and mouse intestinal organoids	STAR Protocols	Organ-on-a-Chip / MPS	Organoid line establishment, chip preparation, seeding and downstream assays.	View protocol ↗
9	Generation of cerebral organoids from human pluripotent stem cells	Nature Protocols	Organoid	Foundational protocol for cerebral organoid generation.	View protocol ↗
10	Generation of kidney organoids from human pluripotent stem cells	Nature Protocols	Organoid	Stepwise differentiation of hPSCs into kidney organoids.	View protocol ↗
11	Efficient genetic engineering of human intestinal organoids using electroporation	Nature Protocols	Organoid	Generation and genetic manipulation of intestinal organoids.	View protocol ↗
12	Intestinal organoid cocultures with microbes	Nature Protocols	Organoid	Microinjection, 2D exposure and analysis of host-microbe organoid cocultures.	View protocol ↗
13	Controlling the polarity of human gastrointestinal organoids	Nature Protocols	Organoid	Methods for manipulating apical-basal polarity in gastrointestinal organoids.	View protocol ↗
14	Establishment of patient-derived cancer organoids for drug-screening applications	Nature Protocols	Organoid	PDO establishment plus semi-automated therapeutic screening.	View protocol ↗
15	Organoid culture systems for prostate epithelial and cancer tissue	Nature Protocols	Organoid	Healthy and cancer prostate organoid generation and culture.	View protocol ↗
16	Generation of proximal tubule-enhanced kidney organoids	Nature Protocols	Organoid	Protocol for improved proximal-tubule specification and kidney organoid maturation.	View protocol ↗
17	CRISPR screens in human neural organoids and assembloids	Nature Protocols	Assembloid / fused organoid	Pooled CRISPR screening in neural organoid and assembloid models.	View protocol ↗
18	Production of human blood-generating heart-forming organoids	Nature Protocols	Organoid	Generation and advanced imaging preparation for heart-forming organoids.	View protocol ↗
19	Long-term versatile culture of functional mouse mammary organoids from single cells	Nature Protocols	Organoid	Long-term culture and expansion of mammary organoids.	View protocol ↗
20	Inducing physiological polarity and CRISPR–Cas9 editing in trophoblast organoids	Nature Protocols	Organoid	Polarity reversal and genome-editing workflows in trophoblast organoids.	View protocol ↗
21	Expansion of induced nephron progenitors and generation of nephron organoids	Nature Protocols	Organoid	Expansion of iNPCs and stepwise differentiation into nephron organoids.	View protocol ↗
22	Cyborg organoids integrated with stretchable nanoelectronics	Nature Protocols	Organoid	Integration of developing organoids with stretchable nanoelectronics.	View protocol ↗
23	Generating human telencephalic brain organoids from single neural rosettes	Nature Protocols	Organoid	Reproducible telencephalic organoids from isolated neural rosettes.	View protocol ↗
24	Generation of human fetal brain organoids and CRISPR engineering	Nature Protocols	Organoid	Fetal brain organoid generation plus CRISPR engineering for tumor modeling.	View protocol ↗
25	Derivation, expansion and cryopreservation of fetal organoids from amniotic fluid cells	Nature Protocols	Organoid	Generation of fetal lung, kidney-tubule and gastrointestinal organoids.	View protocol ↗
26	Generation and characterization of vestibular inner ear organoids	Nature Protocols	Organoid	Step-by-step differentiation and characterization of inner-ear organoids.	View protocol ↗
27	Engineering human hepato-biliary-pancreatic organoids	Nature Protocols	Organoid	Multi-organ hepato-biliary-pancreatic organoid patterning from PSCs.	View protocol ↗
28	A distal lung organoid model	Nature Protocols	Organoid	Generation of distal lung organoids for disease, infection and development studies.	View protocol ↗
29	Single-cell damage in murine intestinal organoid models	STAR Protocols	Organoid	Protocol for targeted single-cell damage in intestinal organoids.	View protocol ↗
30	Serial organoid formation assay using primary colorectal cancer tissues	STAR Protocols	Organoid	Serial organoid formation to assess colorectal cancer stem-cell activity.	View protocol ↗
31	Analysis of neural stem proliferation in cerebral organoids	STAR Protocols	Organoid	Optimized analysis of neural stem-cell proliferation in cerebral organoids.	View protocol ↗
32	Immune cell isolation, organoid generation and co-culture from cryopreserved human intestine	STAR Protocols	Organoid	Integrated immune-cell isolation and intestinal organoid co-culture workflow.	View protocol ↗
33	Robust generation of human midbrain organoids	STAR Protocols	Organoid	Protocol for reproducible generation of human midbrain organoids.	View protocol ↗
34	Generation of vascularized neural organoids by co-culturing mesodermal progenitor cells	STAR Protocols	Organoid	Neural organoid vascularization via mesodermal progenitor co-culture.	View protocol ↗
35	Generation of fused organoids with oligodendroglia and myelin	STAR Protocols	Assembloid / fused organoid	Dorsal/ventral forebrain fusion to create oligodendroglial assembloid-like models.	View protocol ↗
36	Generation of glioblastoma patient-derived organoids and orthotopic xenografts	STAR Protocols	Organoid	Glioblastoma PDO generation and downstream drug-screening workflow.	View protocol ↗
37	Generating patient-derived gliomas within cerebral organoids	STAR Protocols	Organoid	Protocol for integrating patient-derived glioma cells with cerebral organoids.	View protocol ↗
38	Generate mouse oviduct epithelial organoids	STAR Protocols	Organoid	Mouse oviduct epithelial organoid generation, transduction and 3D imaging.	View protocol ↗
39	In vitro establishment and long-term culture of mouse vaginal organoids	STAR Protocols	Organoid	Long-term vaginal organoid establishment and maintenance.	View protocol ↗
40	Measuring neuronal activity in hPSC-derived cerebral organoids on 3D HD-MEA	3Brain	Organoid	Protocol for mounting and electrophysiological recording of cerebral organoids on 3D high-density MEAs.	View protocol ↗
41	Assessing brain organoid network activity	3Brain	Organoid	Application workflow for assessing brain-organoid network activity with BioCAM DupleX and CorePlate.	View protocol ↗
42	Human Lung Organoid Culture Protocol	Bio-Techne	Organoid	Procedure for subculturing, expanding and passaging human lung organoids.	View protocol ↗
43	Human Liver Organoid Culture Protocol	Bio-Techne	Organoid	Procedure for expansion, differentiation and passaging of normal human liver organoids.	View protocol ↗
44	Human Intestinal Organoid Culture Protocol	Bio-Techne	Organoid	Culture and passaging workflow for normal human intestinal organoids.	View protocol ↗
45	Human Gastric Organoid Culture Protocol	Bio-Techne	Organoid	Culture and subculture workflow for normal human gastric organoids.	View protocol ↗
46	Mouse Enteric Organoid Culture Protocol	Bio-Techne	Organoid	Culture, maintenance and passaging protocol for mouse gastric and intestinal organoids.	View protocol ↗
47	Harvesting Organoids for Biochemical Analysis	Bio-Techne	Organoid	Non-enzymatic organoid harvesting workflow for RNA and protein analysis.	View protocol ↗
48	Immunofluorescence Staining of Organoids	Bio-Techne	Organoid	Fixing, embedding, cryosectioning and immunofluorescence workflow for intact organoids.	View protocol ↗
49	Immunostaining in the OrganoPlate	MIMETAS	3D NAM / workflow	Protocol for fixation, permeabilization, blocking and immunostaining of tissues cultured in OrganoPlate devices.	View protocol ↗
50	Developing Organoid Workflows	Sartorius	Organoid	Integrated workflow resource focused on robust and streamlined organoid generation and analysis.	View protocol ↗
51	Growth Factors and Cytokines for Organoid Research	Qkine	Organoid	Organoid culture resource covering defined growth-factor support for reproducible organoid workflows.	View protocol ↗
52	Organoid Culture Handbook	AMSBIO	Organoid	Handbook containing protocols for intestinal, pancreas, liver and stem-cell-derived organoid culture.	View protocol ↗
53	Glioblastoma Cerebral Organoid Protocol	Thermo Fisher Scientific	Organoid	GLICO workflow co-culturing patient-derived glioblastoma cells with human cerebral organoids.	View protocol ↗
54	Organoid and Assembloid Protocol Collection	Thermo Fisher Scientific	Assembloid / fused organoid	Curated organoid and assembloid protocol/publication resource organized by tissue type.	View protocol ↗
55	Cerebral Organoid Culture Protocol	STEMCELL Technologies	Organoid	Four-stage protocol covering embryoid body formation, induction, expansion and cerebral organoid maturation.	View protocol ↗
56	Passaging Intestinal Organoids into Suspension Culture	STEMCELL Technologies	Organoid	Step-by-step protocol for moving intestinal organoids from Matrigel domes into suspension culture.	View protocol ↗
57	CRISPR-Cas9 Genome Editing of Human Intestinal Organoids	STEMCELL Technologies	Organoid	Genome-editing protocol for intestinal organoids using CRISPR-Cas9 RNPs and IntestiCult.	View protocol ↗
58	Human Intestinal Organoid-Derived Monolayers	STEMCELL Technologies	Organoid	Protocol for generating differentiated organoid-derived monolayers, including Transwell and ALI formats.	View protocol ↗
59	Passaging Mouse Intestinal Organoids	STEMCELL Technologies	Organoid	Protocol for preparation, dissociation and passaging of mouse intestinal organoids.	View protocol ↗
60	Establishing Mouse Intestinal Organoid Culture	STEMCELL Technologies	Organoid	Protocol for establishing organoid cultures from isolated mouse intestinal crypts.	View protocol ↗
61	Neural Organoids on High-Density MEAs	STEMCELL Technologies	Organoid	Protocol for preparing cerebral organoids, pharmacological perturbation and electrophysiological analysis on HD-MEAs.	View protocol ↗
62	Neural Organoids on MEA Plates	Axion Biosystems	Organoid	Culture protocol covering MEA preparation, organoid collection, deposition and functional recording.	View protocol ↗
63	Alveolar Organoid Generation	Corning	Organoid	Protocol for generating alveolar organoids using Corning Matrigel Matrix and Transwell permeable supports.	View protocol ↗
64	Best Practices in Spheroid and Organoid Cultures	Corning	Organoid	Practical cell-culture protocol guidance for establishing and maintaining spheroid and organoid models.	View protocol ↗
65	Organoid Model Protocol Resources	Corning	Organoid	Collection of Matrigel and organoid-culture protocol resources across multiple organoid types.	View protocol ↗
66	Organoid Cell Culture Automation Workflow	Tecan	Organoid	Automated organoid culture and analysis workflow using Spark Cyto for kinetic monitoring and reproducibility.	View protocol ↗
67	3D Organoid Image Analysis Workflow	ZEISS	Organoid	Practical image-analysis workflow for organoid lumen, epithelial layers and high-content segmentation.	View protocol ↗
68	3D Cell Culture Guide	Promega	Organoid / Organ-on-a-Chip / 3D culture	Broad guide to 3D culture, organoids, microfluidic organ-on-a-chip models, assays and drug-discovery workflows.	View resource ↗
69	Speedy and Clear 3D Imaging of Organoids	Nikon	Organoid imaging	Application workflow using fluorescence/confocal imaging, deconvolution and image processing for rapid 3D organoid imaging.	View resource ↗
70	Spheroids & Organoids Mechanobiology Workflow	Optics11 Life	Organoid / spheroid mechanobiology	Broader workflow resource for mechanical characterization of spheroids and organoids in near-physiological conditions.	View resource ↗
71	Upscaling Organoid Research for Sharper Biological Insights	Revvity	Automated organoid workflow	Automated organoid/3D workflow covering liquid handling, incubation, monitoring, imaging, analysis and protocol scheduling.	View resource ↗
72	Organoid Generation and Standardization on Gri3D	InSphero	Organoid / 3D culture	Application resource for organoid generation and standardization using the Gri3D microwell platform.	View resource ↗
73	From Patient to Platform	HUB Organoids / Merck	Patient-derived organoids	Step-by-step overview of patient-derived organoid development and scalable organoid screening for drug discovery.	View resource ↗
74	STORganoid Protocol & Workflow	Atelerix	Organoid / spheroid preservation	Workflow for encapsulation, ambient storage, shipment, release and recovery of organoids and spheroids.	View resource ↗
75	Automated Workflows for Complex Organoid Assays	Molecular Devices	Automated organoid culture / screening	Integrated workflow for automated organoid culture, media exchange, compound treatment, imaging and endpoint assays.	View resource ↗
76	Organoid Imaging Workflow for Early Drug Discovery	Leica Microsystems	Organoid imaging	Workflow-driven guide comparing imaging and analysis approaches for complex organoid models in early drug discovery.	View resource ↗
77	High-Throughput Imaging and Analysis of Human Intestinal Organoids	Yokogawa	Organoid imaging / high-content analysis	Scalable workflow combining intestinal organoid monolayers, high-throughput imaging and automated phenotypic analysis.	View resource ↗
78	PhysioMimix Core Organ-on-a-Chip Workflow & Assay Protocol Resources	CN Bio	Organ-on-a-Chip / MPS	PhysioMimix workflow resource covering single-organ, multi-organ and higher-throughput Organ-on-a-Chip models, with validated protocols, assay kits, onboarding guidance and organ-specific multi-chip plates.	View resource ↗
79	W8 Organoid & Spheroid Biophysical QC, Standardisation and Sorting Workflow	CellDynamics	Organoid / Spheroid • 3D Model QC	W8 workflow for label-free biophysical characterisation of organoids and spheroids by size, weight and mass density. Supports culture quality control, standardisation, monitoring protocol-modification effects, drug-response assessment and recovery/sorting of viable 3D-model subpopulations for downstream analysis.	View W8 resource ↗
80	CNS-3D Organoids 96-Well Plate Protocol	28bio	Brain Organoid • CNS-3D	Protocol for receipt and culture of 96-well CNS-3D organoid plates containing iPSC-derived cortical neurons and astrocytes.	View protocol ↗
81	CNS-3D Organoids 384-Well Plate Protocol	28bio	Brain Organoid • CNS-3D	Protocol for receipt and culture of 384-well CNS-3D organoid plates for higher-throughput neural organoid workflows.	View protocol ↗
82	CNS-3D Organoids FLIPR Assay Protocol	28bio	Brain Organoid • Functional Assay	Protocol for handling 384-well CNS-3D organoid plates, preparing FLIPR Calcium 6 reagents and performing the FLIPR functional assay.	View protocol ↗
83	Spheroid & Organoid 3D Imaging Workflow	CrestOptics	Organoid / Spheroid • 3D Imaging	Application workflow for fast, detailed 3D imaging of spheroids and organoids using CrestOptics X-Light spinning-disk confocal and DeepSIM super-resolution systems, including large brain organoids, cortical structures and other complex 3D models.	View resource ↗
84	Chip-S1 Basic Research Kit Protocol	Emulate	Organ-on-a-Chip / MPS	General protocol for using Emulate's Chip-S1 Basic Research Kit, covering the core Organ-Chip culture workflow.	View protocol ↗
85	Compound Distribution Kit Protocol	Emulate	Organ-on-a-Chip / Compound Testing	Control workflow for evaluating compound distribution and exposure in Organ-Chip experiments before quantitative drug studies.	View protocol ↗
86	Emulate Organ-Chip Protocol Library	Emulate	Organ-on-a-Chip / MPS	Protocol library covering Organ-Chip culture, application-specific workflows, compound testing, effluent analysis, imaging and cell-lysate analysis.	View protocol ↗

NAM Protocols

Highlighted Protocols for NAM Models

Protocol Sources

Nature Protocols • Organoids

Nature Protocols • Organ-on-a-Chip

STAR Protocols • Organoids

STAR Protocols • Organ-on-a-Chip

Highlighted Protocols

Growth Factors and Cytokines for Organoid Research

Generate Human Intestinal Organoid-Derived Monolayers

Organoid & 3D Culture Protocol Resources

Culture and analysis of kidney tubuloids and perfused tubuloid cells-on-a-chip

Long-term culture, genetic manipulation and xenotransplantation of human normal and breast cancer organoids

Culture and establishment of self-renewing human and mouse adult liver and pancreas 3D organoids

Microfabrication of human organs-on-chips

Generating and analyzing organ-on-chip using human and mouse intestinal organoids

Generation of cerebral organoids from human pluripotent stem cells

Generation of kidney organoids from human pluripotent stem cells

Efficient genetic engineering of human intestinal organoids using electroporation

Intestinal organoid cocultures with microbes

Controlling the polarity of human gastrointestinal organoids

Establishment of patient-derived cancer organoids for drug-screening applications

Organoid culture systems for prostate epithelial and cancer tissue

Generation of proximal tubule-enhanced kidney organoids

CRISPR screens in human neural organoids and assembloids

Production of human blood-generating heart-forming organoids

Long-term versatile culture of functional mouse mammary organoids from single cells

Inducing physiological polarity and CRISPR–Cas9 editing in trophoblast organoids

Expansion of induced nephron progenitors and generation of nephron organoids

Cyborg organoids integrated with stretchable nanoelectronics

Generating human telencephalic brain organoids from single neural rosettes

Generation of human fetal brain organoids and CRISPR engineering

Derivation, expansion and cryopreservation of fetal organoids from amniotic fluid cells

Generation and characterization of vestibular inner ear organoids

Engineering human hepato-biliary-pancreatic organoids

A distal lung organoid model

Single-cell damage in murine intestinal organoid models

Serial organoid formation assay using primary colorectal cancer tissues

Analysis of neural stem proliferation in cerebral organoids

Immune cell isolation, organoid generation and co-culture from cryopreserved human intestine

Robust generation of human midbrain organoids

Generation of vascularized neural organoids by co-culturing mesodermal progenitor cells

Generation of fused organoids with oligodendroglia and myelin

Generation of glioblastoma patient-derived organoids and orthotopic xenografts

Generating patient-derived gliomas within cerebral organoids

Generate mouse oviduct epithelial organoids

In vitro establishment and long-term culture of mouse vaginal organoids

Measuring neuronal activity in hPSC-derived cerebral organoids on 3D HD-MEA

Assessing brain organoid network activity

Human Lung Organoid Culture Protocol

Human Liver Organoid Culture Protocol

Human Intestinal Organoid Culture Protocol

Human Gastric Organoid Culture Protocol

Mouse Enteric Organoid Culture Protocol

Harvesting Organoids for Biochemical Analysis

Immunofluorescence Staining of Organoids

Immunostaining in the OrganoPlate

Developing Organoid Workflows

Growth Factors and Cytokines for Organoid Research

Organoid Culture Handbook

Glioblastoma Cerebral Organoid Protocol

Organoid and Assembloid Protocol Collection

Cerebral Organoid Culture Protocol

Passaging Intestinal Organoids into Suspension Culture

CRISPR-Cas9 Genome Editing of Human Intestinal Organoids

Human Intestinal Organoid-Derived Monolayers

Passaging Mouse Intestinal Organoids

Establishing Mouse Intestinal Organoid Culture

Neural Organoids on High-Density MEAs

Neural Organoids on MEA Plates

Alveolar Organoid Generation

Best Practices in Spheroid and Organoid Cultures

Organoid Model Protocol Resources

Organoid Cell Culture Automation Workflow

3D Organoid Image Analysis Workflow

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