Complex biological systems are fundamentally determined by the coordinated functions of individual cells.  The transcriptional heterogeneity that drives this complexity is often masked by conventional technologies that only provide bulk transcriptome data.  Although high-dimensional gene expression has been enabled by RNA-Seq, it is currently still a challenge to generate thousands of single-cell NGS libraries in an affordable, high-throughput, and user-friendly manner. To truly deliver on the promise of single-cell biology, a robust technology is required that enables controlled experiments with multiple samples, treatment conditions and time points. 

Here, we present the Illumina | Bio-Rad Single-Cell Sequencing Solution. This new platform pairs Bio-Rad’s Droplet Digital Technology with Illumina’s NGS library preparation and analysis technology to provide a comprehensive workflow for single-cell analysis. Single cells are individually partitioned into subnanoliter droplets on a disposable cartridge on the one-touch ddSEQ Single-Cell Isolator. The cartridge can accommodate multiple samples, and multiple cartridges can be processed in parallel to isolate tens of thousands of cells in a matter of minutes. Cell lysis and cell barcoding occurs inside individual droplets, and single-cell-barcoded RNA-Seq libraries are subsequently prepared with using Nextera Technology. Data analysis is conducted via BaseSpace, Illumina’s cloud-based genomics computing environment.

This droplet-based method is agnostic to mammalian cell size, enabling unbiased profiling of diverse cell populations.  Additionally, because the time from culture to lysis is on the order of a few minutes, transcriptional signatures are not affected by lengthy experimental workflows allowing for acute transcriptional responses to be detected and tracked by time course.  This scalable, cost-effective, fast, simple, reproducible and robust single-cell NGS sample prep methodology will enable more researchers to apply the sensitivity and precision of RNA-Seq to questions in single cell biology.