The next big leap in single cell: Introducing Quantum Barcoding

In the rapidly evolving landscape of single cell RNA sequencing, researchers still face technological limitations that pose challenges to scalability, efficiency, and cost-effectiveness. Scale Bio's novel Quantum Barcoding technology represents a fundamental rethinking of how we approach single cell analysis, greatly expanding the number of cells that can be analyzed with massively parallel barcoding approaches, while simultaneously improving workflow efficiency, for the most user-friendly single cell workflow.  

Innovating with Scale in Mind 

Some technologies are fundamentally limited in the number of samples that can be run. This is because as the number of samples increases, the time to prep and process libraries also increases with each added sample (as well as the cost). However, a combination of innovations from Scale Bio enables more efficient scaling of sample numbers. The first is on the sample prep side. With ScalePlex technology, the fixation and multiplexing process of samples is greatly streamlined, allowing you to fix and pool up to 96 unique samples simultaneously in only a hour.  ScalePlex pools can then be used with the built-in barcodes (96 barcodes) of our single cell RNA-seq kits to enable up to 9,216 samples per run (96 x 96 = 9216). 

The second innovation is Quantum Barcoding technology, which massively increases the barcoding space compared to standard combinatorial indexing without any additional handling steps, which we’ll turn to next. 

Reimagining the (Micro)well 

At the heart of Quantum Barcoding technology is a novel plate with unique microwell architecture. Unlike other combinatorial indexing strategies that require additional split-and-pool steps for increasing the barcode space and therefore the number of unique cells that can be analyzed, Quantum Barcoding employs specially designed microwell-within-a-well plate paired with oligo-coated beads carrying unique barcodes. The simplicity of this approach – allowing beads and cells to settle into the tens of thousands of microwells that are contained within each “macro” well – consolidates many levels of barcoding into one streamlined operation, cutting the amount of hands-on time by over 75%.  

Breaking Performance Barriers 

Quantum Barcoding technology is powering data generation for the 100 Million Cell Challenge, as well as the newest platform, QuantumScale, by enabling:  

• Ultra-high throughput: Process up to 2 million cells in just 1.5 days 

• Efficiency gains: Reduce hands-on time to merely half a day 

• Cost effectiveness: As low as 1 cent per cell, and under $100 per sample when running hundreds of samples 

• Streamlined workflow: Fewer pipetting steps while greatly expanding the total number unique cells that can be analyzed 

The Power of Platform Flexibility  

Unlike legacy chip-based approaches, which are inherently limited by channel configurations and microfluidics, the QuantumScale platform isn't constrained by channels on a chip. This fundamental difference enables exciting opportunities, future improvements and innovation. The technology isn’t limited to only RNA – it also powers single cell protein profiling, with other modalities coming soon. Scale Bio has created a platform that can evolve and expand with the growing demands of single cell research.

QuantumScale Single Cell RNA-seq is currently offered in our Service Lab. This is a great way to get that large-scale (or any scale!) project you had on your mind done with our expert technicians without waiting. You can also register your interest for early access to QuantumScale Single Cell RNA kits.