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Organoid Culture in micro-beads

Microbead-based microfluidics is a powerful technique that generates highly monodispersed picoliter-sized beads into a continuous phase. This method has been successfully adapted to cell culture to encapsulate cells in micron size hydrogel beads. The main advantages are reduced costs related to miniaturization, high reproducibility, and high throughput screening capacities. 


Prostate organoid after 7 days incubation. Visualization under fluorescent microscope

Benefits of Organoid Culture

Single-cell embedded in microbeads: Each single microbead is considered as a single ‘bioreactor’ for 3D cell culture.

Clonal generation of organoids: Each single encapsulated cell gives rise to an organoid derived from clonal origin.

Monodispersity: The High Throughput (HT) formation of beads (2000 microbeads/min) of controlled size, shape, composition and cell distribution allows the generation of homogeneous and ‘standardized’ organoids.

Reduced volume of matrix: 2 to 3 times less ECM (Extra Cellular Matrix) for instance than traditional cultures. As an example, 350 µl ECM (one well of a LabTek 4-chambers slides) allows to produce 42.800 microbeads with a diameter of 250 µm).

Easy handling: Recovery of organoids in culture media for further analysis.

Storage: Microbeads with embedded organoids can be cryopreserved for long periods without altering organoids achitecture and function.

Biological relevance Low High High
Control over 3D culture / Low High
Easy handling Yes No Yes
Clonality No No Yes
Transfection efficiency High Low High
Long term storage Yes No Yes
High throughput Yes No Yes
Cost Low High Medium

Applications of Organoid Culture

Functional genomic studies: Controlled organoid generation combined to 3D iRNA-based electroporation in beads opens new perspectives for flow-based HT genetic screening and functional genomic application. The transfection efficiency is optimized by modulating microbead size and ECM concentration. The reduced amount of ECM surrounding organoids constitutes a permissive 3D environment that facilitates transfection. PubMed link ».

Tissue development and tumorigenesis: Collecting microbead-containing organoids at different stages allows performing multi-omics analysis of organoid development or carcinogenesis. PubMed link »

Organoids / tumoroid-based drug assays: Flow-based strategies prove very convenient for the future HT Screening in 3D models and identification of potential RNAi therapeutics. PubMed link »

3D Tool-box: Floating 3D organoids in beads can easily be aspirated, dispensed and sorted by large-particle fluorescence-assisted cell sorting. This flow-based technology opens up broad applications in the field of 3D culture. PubMed link »

Setup for organoids generation and cryopreservation

Informative bibliography

[1]    Laperrousaz, B., Porte, S., Gerbaud, S., Ville, H., Gidrol, X., Hourtane, V., & Picollet-D’hahan, N. (2018). Direct transfection of clonal organoids in Matrigel microbeads: a promising approach toward organoid-based genetic screens, Nucleic Acid Research, 1–13.

[2]    Dolega, M. E., Abeille, F., Picollet-D’hahan, N., & Gidrol, X. (2015). Biomaterials Controlled 3D culture in Matrigel microbeads to analyze clonal acinar development. Biomaterials, 52, 347–357.

[3]    Picollet-D’hahan, N., Dolega, M. E., Freida, D., Martin, D. K., & Gidrol, X. (2017). Deciphering Cell Intrinsic Properties: A Key Issue for Robust Organoid Production. Trends in Biotechnology, 35  (11), 1035–1048.

[4]    Picollet-D’hahan, N., Dolega, M. E., Liguori, L., Marquette, C., Le Gac, S., Gidrol, X., & Martin, D. K. (2016). A 3D Toolbox to Enhance Physiological Relevance of Human Tissue Models. Trends in Biotechnology, 1–13.

Application components

MFCS-EZ: Mikrofluidisches Flusskontrollsystem

MFCS-EZ, Microfluidic flow control system

An unique 4 channel microfluidic flow control system
Key features:
– Easy to install and use
– Many automation possibilities
– Field proven technology and superior quality

FRP flow-rate


A unique flow-rate measurement solution.
Key features :
– High repeatability
– Tunable to your liquids
– Easy to set up and use

Logo dSurf


dSURF is a high-performance fluorosurfactant dedicated to microdroplet generation.
Key features:
– Biocompatible
– Best performances
– Efficient in strong experimental conditions

Courtesy of Biomicrotechnology and functional genomics (BIOMICS), CEA, Grenoble, FRANCE.
In collaboration with Leti, a technology research institute at CEA Tech
The Organoids-on-Chip project has received funding from the EU’s H2020 research and innovation program (N°766884) (Read more)

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