Single-cell analysis enables the investigation of characteristics of individual cells in a homogeneous population, facilitating genomic, transcriptomic, proteomic and metabolomic studies at the single-cell level. By studying individual cells in a heterogeneous mixture, it is possible to examine rare cell types and to make discoveries that would be difficult to see in a bulk cell population.

With growing applications in research and medicine, multiple technologies have emerged for the collection and/or analysis of individual cells with characteristics of interest. Each technology is suited for a subset of research and production applications. Droplet-based cell analysis is most often associated with transcriptome analysis through the sequencing of RNA. This enables analysis of which genes are being expressed at a given time at single-cell resolution, and can provide insights into disease, physiology and immunology. RNA is not as stable as DNA and is more sensitive to degradation. Droplet-based cell analyzers are able to process cells quickly and gently to maintain native expression profiles.

Droplet-based single-cell analysis technology is relatively new, with the first commercial systems released in 2016. The principles behind the high-throughput sequencing of RNA from single cells originate from a method developed at Harvard University. The technology facilitates preparation of over 15,000 cells per hour.

While each instrument on the market varies in its approach, they share some common characteristics. The instruments use chip-based microfluidics technologies to generate aqueous droplets in the picolitre-volume range and micron-sized; each droplet encapsulates a single cell. The systems and their respective protocols each incorporate reverse transcription and barcoding. Reverse transcription, which is performed by the enzyme reverse transcriptase (RT), makes cDNA copies of RNA. This is a typical step in RNA analysis, as current DNA sequencing technology is far more advanced than RNA sequencing.

Barcoding incorporates a unique molecular identifier (UMI) onto reverse transcription primers, so that the resulting cDNA sequences from each cell can be differentiated in downstream analysis. Barcoded primers are generally encapsulated together with a cell in a droplet, where ligation of the primer to the RNA takes place. Depending of the instruments, the reverse transcription reaction takes place either within the droplet (in which case RT is also encapsulated) or after the droplet is broken. Most systems do not incorporate sequencing functions, requiring subsequent sequencing using a dedicated sequencer.

Only a handful of companies currently participate in the droplet-based single-cell analysis market. 1CellBio, which was the first to market with its InDrop system, is a spinout from Harvard University. Other available instruments are the Chromium System from 10x Genomics, the Nadia System from Dolomite Bio, and the Single-Cell Sequencing Solution, which is a collaborative effort between Illumina and Bio-Rad Laboratories.

Droplet-Based Single-Cell Analyzers at a Glance:

Leading Vendors

• 10x Genomics
• Illumina/Bio-Rad Laboratories (collaboration)
• 1CellBio
• Dolomite Bio

Largest Markets

• Academia
• Pharmaceutical and Biotechnology
• Hospital and Clinical