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Library

Knowledge Base

Welcome to the PeptiMatrix™ Knowledge Base. Here you will find everything you need to make the most of our technology, including FAQs, SOPs, Application Notes, and Video Demos. Explore the resources below or use the links to jump directly to the section you need.

SOPs

Our validated SOPs provide clear, ready-to-use protocols for working with PeptiMatrix™ hydrogels. They enable you to focus on generating meaningful data rather than spending time optimising methods.

Encapsulating cells in PeptiMatrix™ hydrogels

This SOP provides a step-by-step guide to encapsulating cells within PeptiMatrix hydrogels to create 3D culture models. It outlines preparation, mixing, and handling procedures to ensure consistent and reproducible results.

Coating well-plates with PeptiMatrix™ hydrogels

This SOP describes how to coat well plates with PeptiMatrix hydrogels for use as a biologically relevant surface for cell seeding. It enables a “2.5D” culture setup, allowing cells to grow on top of the hydrogel while maintaining interaction with a defined extracellular matrix environment.

Extracting cells from PeptiMatrix™ hydrogels

This SOP details how to extract cells from PeptiMatrix hydrogels in a gentle and cell-friendly manner. It provides guidance on recovering viable cells for re-seeding, imaging, or downstream molecular analysis.

LIVE/DEAD Stain for cell viability

This SOP describes how to perform LIVE/DEAD staining to assess cell viability in 3D PeptiMatrix cultures. The method enables visualisation of live and dead cells using fluorescent dyes, supporting evaluation of encapsulation efficiency and culture conditions.

CellTiter-Glo® 3D assay for cell viability

This SOP explains how to perform the CellTiter-Glo® 3D assay to assess cell viability within PeptiMatrix hydrogels. It provides detailed steps for reagent preparation, sample handling, and luminescence measurement to quantify metabolic activity in 3D cultures.

PrestoBlue™ assay for cell viability

This SOP describes how to perform the PrestoBlue™ assay to evaluate cell viability in PeptiMatrix hydrogels. It outlines the procedure for reagent preparation, incubation, and fluorescence measurement to assess metabolic activity in 3D cultures.

ICC staining of cells in PeptiMatrix™ hydrogels

This SOP outlines how to perform immunocytochemistry (ICC) staining on cells cultured within PeptiMatrix hydrogels. It provides guidance on fixation, permeabilisation, antibody incubation, and imaging to visualise specific cellular markers within 3D environments

RNA extraction from cells in PeptiMatrix™ hydrogels

This SOP details how to extract high-quality RNA from cells encapsulated in PeptiMatrix hydrogels. It provides guidance on efficient cell lysis, hydrogel dissolution, and RNA purification for downstream gene expression analysis.

Videos

Explore our collection of video demonstrations showing key PeptiMatrix™ protocols in action. These step-by-step guides complement our SOPs and help you quickly master essential techniques.

Encapsulating cells in PeptiMatrix hydrogels

This video demonstrates how to encapsulate cells within PeptiMatrix hydrogels to create 3D culture models. It provides a visual guide to the key steps outlined in the "Encapsulating cells in PeptiMatrix hydrogels" SOP, helping you achieve consistent and reproducible results.

Extracting cells from PeptiMatrix hydrogels

This video demonstrates how to extract cells from PeptiMatrix™ hydrogels using a gentle, cell-friendly process. It complements the "Extracting cells from PeptiMatrix hydrogels" SOP and shows how to recover viable cells for re-seeding or downstream analysis.

3D Bioprinting with PeptiMatrix hydrogels

This video demonstrates the compatibility of PeptiMatrix™ hydrogels with SPT Labtech's dragonfly® discovery liquid handler, showing how automated dispensing can reduce variability, improve reproducibility, and streamline high-throughput 3D model generation.

FAQs

We've gathered answers to the most frequently asked questions about our products in one convenient place, making it easier for you to find the information you need quickly and easily.

Are your hydrogels truly 100% animal-free?

Yes—our hydrogels are completely animal-free, not just in the final product but throughout the entire manufacturing process. We use no animal-derived materials at any stage, ensuring a fully defined, ethically responsible alternative to traditional animal-based matrices. This means you can trust that our products support both scientific reproducibility and sustainability from start to finish.

What is the gelation mechanism of your hydrogels?

Our hydrogels use a pH-dependent gelation mechanism. The material is supplied as a precursor gel solution that transitions into the final hydrogel upon mixing with the cell suspension—no cross-linking or temperature change required. This gentle, room-temperature process is highly cell-friendly, and the shear-thinning properties of the gel allow easy plating or manipulation even after gelation.

 

How long can you culture cells for in the hydrogels?

Culture duration depends on the cell type and seeding density, but PeptiMatrix hydrogels can support long-term culture. Under appropriate conditions, cells have been successfully maintained for more than 30 days.

 

How do you extract cells from the hydrogels?

Cells can be extracted from PeptiMatrix hydrogels using a simple, gentle process. By diluting the gel in PBS, the peptide concentration drops below the critical gelation threshold, allowing the matrix to dissolve and cells to be recovered. A detailed cell extraction protocol is freely available in our Knowledge Base.

Which cell lines and tissue types are compatible with your hydrogels?

PeptiMatrix hydrogels are compatible with a wide range of cell lines and tissue types, including epithelial, stromal, and cancer-derived cells. For specific examples and recommendations, please visit our Products page for a full list of validated applications.

What are the storage conditions and shelf-life of your hydrogels?

PeptiMatrix hydrogels are stable at ambient temperature for short periods during shipping. On receipt, they should be stored at 4 °C and used within 3 months for optimum performance. While some customers have reported successful use up to 6 months, this is not guaranteed.

What is the pore size of the hydrogels?

The exact pore size of PeptiMatrix hydrogels is difficult to define, as conventional measurement methods often disrupt the hydrated structure of hydrogels. However, diffusion through PeptiMatrix hydrogels is excellent, allowing nutrients and gases to reach encapsulated cells while enabling efficient removal of waste products.

How do I remove or avoid bubbles in the gels?

Small air bubbles may appear in the gel after shipping. To remove them, centrifuge the gel at 600 × g for 1 minute before use. To minimise air introduction during cell encapsulation, use reverse pipetting techniques. More detailed guidance is available in our "Encapsulating cells in PeptiMatrix hydrogels" SOP in the Knowledge Base.

Are the hydrogels compatible with bioprinting?

Yes, PeptiMatrix hydrogels are compatible with extrusion-based bioprinters due to their shear-thinning properties, which allow smooth flow through printer nozzles and rapid recovery after deposition. For more information, see our recent Application Note with SPT Labtech, available in the Knowledge Base.

Are the hydrogels compatible with organ-on-chip platforms?

PeptiMatrix hydrogels perform well under fluid flow and have been successfully used in organ-on-chip and microphysiological systems. A recent publication from Wageningen University & Research using HepaRG cells has recently been accepted and a link to the full formatted version will be available soon on our Publications page.

Application Notes

Our Application Notes showcase how PeptiMatrix™ hydrogels are applied in real research settings. Each note highlights specific experimental setups, cell types, and outcomes, demonstrating how PeptiMatrix™ supports reliable 3D culture, imaging, and assay compatibility across diverse applications.

Advancing 3D Cell Culture: Automated positive displacement dispensing of MCF7 and HepG2 cells, mixed with PeptiMatrix™ Hydrogel

We collaborated with SPT Labtech to demonstrate the compatibility of our PeptiMatrix™ hydrogels with the dragonfly® discovery liquid handler for automated 3D cell culture. Together, we evaluated the system using MCF7 (breast cancer) and HepG2 (liver cancer) cell lines, showing how automated dispensing can reduce variability, improve reproducibility, and streamline high-throughput 3D model generation.

Building Better Brain Cell Models with PeptiMatrix™ Hydrogels

Explore how PeptiMatrix™ hydrogels support 3D culture of brain cell lines, offering an animal-free, tunable, and reproducible platform that mimics the softness of neural tissue. This study shows how BT-16, SH-SY5Y, and U87 cells thrive in PeptiMatrix™, producing more physiologically relevant models for brain research.

 

GET IN TOUCH

If you would like to know more about our technology, or would like to be one of the first to trial one of our products in your work, please get in touch!

PeptiMatrix Limited,

Biodiscovery Institute,

Science Road,
Nottingham,

NG7 2RD, UK

E: info@peptimatrix.com

T: +44 (0) 7599 442871

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