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Encapsulation of Cells in Individual Hydrogel Scaffolds

Encapsulation of Cells in Individual Hydrogel Scaffolds

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Cell Encapsulation in Agarose

3D Cell Culture

Novel protocol development- custom single cell hydrogel encapsulation

What are hydrogels?

Hydrogels are semi-solid materials composed of a network of insoluble hydrophilic polymers which absorb water. Hydrogels can either be naturally occurring, such as agarose, acrylamide, or collagen; or chemically synthesised, such as polyethylene glycol.

Hydrogels in single cell research


Hydrogels can provide solid-phase scaffolds for cells while allowing diffusion of dissolved nutrients and gases throughout. Therefore, cells encapsulated within hydrogel scaffolds can remain viable for extended periods of time or even proliferate throughout the hydrogel matrix, making hydrogel encapsulation of cells a versatile tool for understanding biological systems.

Encapsulation of cells within hydrogel scaffolds can be performed on the Nadia instrument and novel protocols and workflows for cell-encapsulation within hydrogels can be developed and optimized with Nadia Innovate or the Nadia Go.

Flow focusing on the Nadia microfluidic chip produces hydrogel droplets at high throughput. This technique can be used to encase cells in spherical hydrogel scaffolds.


Encapsulating cells in agarose scaffolds: nadAROSE

  Agarose is a naturally occurring polysaccharide hydrogel, extracted from certain types of red seaweed. It has excellent biocompatibility, thermo-reversible gel behaviour, is non-toxic and low-cost, all of which make it a versatile and popular material for life-sciences applications [1].

Agarose, when solidified into spherical scaffolds, can provide a solid support to cells encapsulated within, while allowing diffusion of nutrients and gases and cell secretions. Agarose scaffolds can therefore display some of the properties of the native physiological environment of living cells [4]. For this reason, cells encapsulated in agarose can remain viable for extended periods of time within the three-dimensional microenvironments.

Cell-containing agarose scaffolds can be used in the following applications:

  • Flow cytometry
  • Cell secretion studies
  • Cell-cell interactions
  • Microbial cell culture

Two living, differentially-stained, cells were encapsulated together in an agarose bead on the Dolomite Bio Nadia Innovate platform. (in blue: Hoechst-stained HEK cell, in green: Calcein-stained 3T3 cell).


The nadAROSE kit provides a simple, low-cost commercial solution for the encapsulation of single cells in individual agarose micro-scaffolds in a high throughput, reproducible manner on the Nadia instrument. Due to the high-throughput the cost per cell is drastically reduced compared to other methods.

The nadAROSE kit is compatible with many downstream applications. The cell-containing agarose scaffolds are compatible with flow cytometry instruments and could also be used for cell-cell interaction studies, cell secretome studies or for microbiological cell culture, to name a few. Whatever the application, you can do it while maintaining single cell identity. The nadAROSE kit also provides the necessary reagents cells from their agarose scaffolds for further cell analysis or merging of workflows.

App Note CTA
Visit the webpage Download the nadAROSE
application note
Read the datasheet

Encapsulating cells in collagen-based scaffolds for 3D culture: nadia3D

3D cell culture

3D cell cultures, such as organoids and spheroids, have distinct advantages over 2D cultures for diverse cell and tissue types as they more closely mimic the natural environments of the cell. The first step in many 3D cell culture protocols is to seed single or multiple cells into a hydrogel matrix or scaffold.

nadia3D kit

The nadia3D kit provides a simple, commercial solution for the encapsulation and culture of single-cells in individual collagen-based micro-scaffolds in a high-throughput and reproducible manner using the Nadia instrument.

Few other methodologies can quickly and reproducibly generate hundreds of thousands of single cell 3D collagen-based scaffolds, all whilst maintaining single cell identity. The Nadia’s versatility means this technique can be applied to cells of diverse sizes and morphologies, including large, multinucleated cells such as cardiomyocytes. Once the cell-containing scaffolds are produced, they are separated from the oil phase and can then be perfused with a variety of culture media for 3D cell growth studies.

Cell-containing collagen-based scaffolds can be
used in the following applications:

  • Spheroid growth
  • Organoid production
  • Drug discovery, screening and evaluation
  • Disease models
  • Developmental studies
Visit the webpage  Watch the webinar Read the datasheet

Nadia Innovate and Nadia Go – enabling the development of custom single cell hydrogel encapsulation

Using Dolomite Bio’s core pressure-controlled microfluidics technology, the Nadia Innovate and Nadia Go, enable the development of user-defined single cell protocols and applications. For high throughput parallel operation, newly developed protocols can be transferred to the the Nadia Instrument. Alternatively, for projects that only require single lane chips, we have recently developed the Nadia Go, enabling access to the customizable features of the Nadia Innovate without purchasing a Nadia Instrument alongside it.

By allowing users to control parameters such as droplet size, droplet frequency, temperature, agitation and timing, innovation is unlocked. Design a protocol for cell encapsulation in your own hydrogel formulation with the Nadia Innovate or the Nadia Go.

Visit the Nadia Innovate product page

Visit the Nadia Go product page

Customizable parameters on the Nadia Innovate and Nadia Go

Ways to get in touch



[1] Luo R-C. and Chen C-H., “Structured Microgels through Microfluidic Assembly and their Biomedical Applications”, Soft. 2012 Dec;1;1-23
[2] Smith BH, Gazda LS, Conn BL, Jain K, Asina S, Levine DM, et al. Three-Dimensional Culture of Mouse Renal Carcinoma Cells in Agarose Macrobeads Selects for a Subpopulation of Cells with Cancer Stem Cell or Cancer Progenitor Properties. Cancer Res. 2011 Feb 1;71(3):716–24.
[3] Li Y, Kumacheva E. Hydrogel microenvironments for cancer spheroid growth and drug screening. Sci Adv. 2018 Apr 1;4(4):eaas8998.
[4] Joseph JS, Malindisa ST, Ntwasa M. Two-Dimensional (2D) and Three-Dimensional (3D) Cell Culturing in Drug Discovery. In: Cell Culture [Internet]. 2018 [cited 2019 Sep 19]. Available from: