Abstract

Quantitative Profiling of Large and Complex Single Cell Populations

Grace Zheng, Senior Scientist, 10x Genomics

Understanding of complex biological systems requires the knowledge of their individual components. The ability to profile a large number of cells is becoming increasingly important for rare cell detection without complicated enrichment procedures, and for comprehensive classification of biological systems. However, existing single cell RNA-sequencing (scRNA-seq) methods have limited throughput, and computational analysis is not scalable.

The Chromium single cell system from 10x Genomics uniquely enables large-scale scRNA-seq studies. The updated microfluidics and biochemistry can capture >70% of loaded cells with a low doublet rate (<1% per 1000 cells), facilitating the profiling of precious and rare cell populations. 80k cells can be recovered in droplets per 7 min run, and the sequencing libraries can be made within 7 hours, enabling high sample and cell throughput. These libraries are compatible with the HiSeq4000 sequencer, currently the most cost effective sequencing platform provided by Illumina. The analysis pipeline, Cell Ranger, is optimized for efficient processing of sequencing data to produce per-cell gene expression matrices and an automated cell clustering analysis.

We demonstrate the scalability of the Chromium single cell system by profiling a million neurons from murine brains. Major neuronal and non-neuronal cell types from different layers of cortex, hippocampus and subventricular zones were detected. Diverse, yet rare interneurons were readily detected without FACS enrichment, demonstrating the power of Chromium system in profiling complex populations and detecting rare cell types. Comparison of neuronal sub-populations at 2 developmental time points reveals interesting dynamics between progenitors and mature neurons, providing a rich resource for the neuroscience community. We envision that this technology will enable widespread adoption of high-throughput single cell mRNA analysis, and accelerate the characterization of diverse developmental systems as well as tumor samples in basic and clinical research.