Abstract

The human body comprises trillions of cells, all containing identical DNA, yet exhibiting diverse functions. This cellular heterogeneity is better understood through RNA analysis rather than DNA sequencing. Single-cell RNA sequencing (scRNA-Seq) has revolutionized this field, with Drop-seq emerging as a pivotal technique. Drop-seq utilizes droplet-based microfluidics to encapsulate individual cells with functionalized beads in nanoliter-sized droplets, enabling high-throughput RNA analysis. Despite its advantages, Drop-seq faces challenges such as low yield and difficulty in monitoring the encapsulation process.

Sensific’s technology addresses these limitations by enhancing the efficiency and resolution of Drop-seq. The sensors provide optimal process monitoring, allowing direct control over droplet rate and distribution. This technology eliminates reliance on statistical encapsulation, ensuring nearly 100% purity by identifying and sorting correctly configured droplets in real-time.

Consequently, Sensific’s product integration significantly improves the accuracy and throughput of single-cell RNA sequencing as of various other applications, offering a robust solution for cellular analysis. This advancement not only simplifies the setup adjustment but also enriches the desired droplet population, making it a transformative approach in the field of biotechnology.

 

What is Drop-seq?

Drop-seq is a technique for single-cell RNA sequencing (scRNA-Seq) that uses droplet-based microfluidics to encapsulate individual cells with functionalized beads in nanoliter-sized droplets. This method allows for high-throughput RNA analysis, significantly reducing experimental time and increasing throughput.

What are the challenges with traditional Drop-seq?

Low yield – only about 1% of cells are correctly encapsulated with a bead, leading to low sequencing efficiency.

Difficulty in monitoring the encapsulation process, which relies on statistical encapsulation.

Sensific’s enhancements with ODIN

• Improved efficiency and resolution: Sensific’s technology enhances Drop-seq by providing optimal process monitoring and direct control over droplet rate and distribution. 

• Real-time sorting: The sensors identify and sort correctly configured droplets in real-time, ensuring nearly 100% purity.

• Increased encapsulation efficiency: Efficiency is improved from less than 1% to approximately 14%, allowing more cells to be sequenced.

• Cost reduction: Reagent costs are reduced by a factor of 100, lowering overall experiment costs by up to 20%.

• Shorter experiment duration: The improved method increases the rate of correctly configured droplets, reducing the time required for experiments.

• Minimized cellular stress: Reduced experiment duration minimizes stress-induced changes in RNA composition within cells.

• Reduced background RNA noise: Background noise from free RNA is reduced by 99%, improving sequencing accuracy.

Versatile applications of Sensific's technology

Sensific’s technology can be applied to various assays beyond Drop-seq, including the generation of monoclonal cultures, analysis of cell populations, and studies on cell-cell interactions. The ODIN system allows for up to three fluorescence modes to be connected and imaged simultaneously, increasing process robustness and enabling the detection of additional markers.

Integrated platform ZEUS

ZEUS combines all elements of the setup into a compact benchtop device with fully integrated software, automating many process steps for maximum convenience and efficiency. It includes features like a quick-mount system for microfluidic channels, minimizing dead volume and making it ideal for small sample volumes.

Impact and future prospects

Sensific’s advancements in Drop-seq technology provide significant improvements in efficiency, cost, and time savings. The technology has broad applications in biotechnology, including personalized cancer therapies, Alzheimer’s research and drug development.These enhancements make Sensific’s technology a transformative approach in the field of single-cell RNA sequencing and biotechnology.

 

Please contact us for the detailed version of this application note.