Omics

Rapid Automation of CS Genetics’ Single-Cell Sequencing to Unlock Novel Applications

Single-cell sequencing workflows are often complex and require specialised operators, limiting broader adoption. Integrating CS Genetics’ SimpleCell™ workflow with TTP’s modular LINK system, TTP have demonstrated a configurable, ‘plug-and-play’ consumable, making CS Genetics’ single-cell sequencing accessible and scalable for wider applications.

Client

CS Genetics

Industries

Life Science, Omics

Context

The need to partition cells via droplet generation or multiple rounds of pipetting for combinatorial barcoding limits applications and the wider adoption of many single-cell workflows. CS Genetics’ technology simplifies single-cell sequencing workflows to the point where – with automation – they could be adopted in a variety of industrial settings.

Solution

By implementing CS Genetics’ SimpleCell™ workflow on TTP’s LINK – our modular system for rapid automation-friendly assay development – we demonstrated the automation of CS Genetics’ technology and configuration of a custom ‘plug-and-play’ consumable.

Result

The success of demonstrating the automation of the SimpleCell™ workflow highlights the versatility and potential, bringing a range of industrial production and quality assurance applications within the reach of CS Genetics’ technology.

A step towards plug & play single-cell library prep

Current single-cell workflows rely on droplet generation or multiple pipetting rounds for combinatorial barcoding. This limits applications and means that highly trained operators with specialized equipment are required to run single-cell workflows. CS Genetics is simplifying single-cell sequencing workflows, enabling broader applications.

By partnering with TTP, and leveraging our advanced automation expertise, CS Genetics have made the first steps in automating its SimpleCell™ single-cell library preparation platform. The data presented here represents a first step toward creating a truly plug-and-play single-cell library preparation system.

CS Genetics SimpleCell™ Kinetic Confinement technology provides kit-based single cell analysis of gene expression and other cellular/multi-omic readouts. The technology leverages novel, bifunctional indexing reagents to deliver index sequences directly to single cells; and then uses a biophysical process known as ‘Kinetic Confinement’ to perform high-fidelity indexing of target molecules, across thousands of cells simultaneously.

However, the automation of a biological assay into a plug-and-play instrument requires the construction of iterative ‘breadboards’ to build and test potential solutions, often with multiple costly iterations of custom injection-moulded consumables and a complete set of mechanical and electronic systems.

TTP have developed the LINK platform to streamline this initial phase of plug-and-play assay automation projects.

  1. Select the pot combinations required for the assay.
  2. Place the consumable cartridge into LINK.
  3. Ensure the correct functional modules are present.
  4. Run the assay.

LINK is a flexible and modular instrument with a library of modules and consumables to enable the rapid development of automation-friendly assays. Although not a breadboard system, LINK still provides flexibility in development and functions with a variety of pot combinations and processes (thermocycling, incubation, bead clean-up, etc). All functions and pots are swappable to facilitate protocol and process changes without the need to tweak consumable designs.

In this way, LINK reduces the cost and risk associated with integrating complex biological processes in automated instrumentation. The biology-consumable combination identified on LINK can be translated directly into the product design, reducing development time while generating representative biological data early in a project’s timeline.

The data below demonstrates the feasibility of a ‘plug-and-play’ single-cell instrument, opening a range of applications for CS Genetics’ technology.

PBMCs from a healthy donor were analyzed using CS Genetics’ SimpleCell on TTP’s LINK. In addition to identifying major immune cell types, we also observed a clear difference in the distribution of RNA transcripts between singlets, multiplets, and negatives as expected, indicating the unambiguous detection of multiplets and negatives.

In biological model generation, single-cell sequencing can verify genomic edits, track insertion expression, and identify mosaicism. Off-target effects can also be detected to ensure uniform product expression before release.

A simple, user-friendly plug-and-play instrument could also enhance cell-based product manufacturing (e.g., cell and gene therapy), by monitoring cell expression and uniformity in bioreactors to detect unwanted subpopulations or contaminants, thereby maintaining product quality.

This type of technology also supports final-stage Quality Control for cell and gene therapies, confirming the therapeutic product’s genetic and expression profiles for safety and efficacy.

Additionally, automation could enable the deployment of CS Genetics’ technology in hospitals for diagnostic use, for example, to offer insights into tumor heterogeneity and rare mutations, or to track tumor evolution. In infectious disease, it could profile immune responses, guiding treatment strategies.

Coupling CS Genetics’ SimpleCell platform with LINK, TTP’s automation solution, demonstrates the first steps towards transformative access to single-cell sequencing for a diverse set of industries requiring deeper insights into genetic and cellular diversity.

Figure 1. PBMCs were isolated from a healthy donor and were analysed using CSGX SimpleCell on TTP’s Link. Shown above is a UMAP and a clustered dot plot of all cells identified as major immune cell types. Each point on the UMAP represents one single cell, coloured according to cell type: Marker genes for identification of major peripheral blood cell type: T cells (CD3E+ve and IL7R+ve), CD4 T cells (CD3E+ve and CD4 +ve), CD8 T cell (CD3E+ve,CD8A+ve and NKG7+ve), NK cells (CD3E -ve,NCAM1+ve), monocytes (TCF7L2+ve and FCGR3A+ve) and B cells (MS4A1+ve).
Figure 2. Cells from a 1:1 mixture of human (HEK 293T) and mouse (NIH/3T3) were profiled using the Simple Cell CSGX 3’ on link. Green colour dots indicate single cell transcripts, blue colour dots indicate multiple transcripts, and grey colour dots indicate doublets that are positive for both species. We also observed a clear difference in the distribution of RNA transcripts between singlets, multiplets, and negatives as expected, indicating the unambiguous detection of multiplets and negatives.

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