High throughput single cell analysis

Individual cell heterogeneity within a population has invalidated historic classification methods based on macroscopic considerations and given rise to new evaluation techniques based on single cell transcriptional signature. In this context, thanks to high throughput screening capacities, easy fluid handling and reduced costs related to device miniaturization, microfluidics has emerged as a powerful tool for single cell manipulation and analysis.

Droplet Microfluidics

Recent analysis of healthy and diseased tissue homogeneous at the macroscopic scale revealed strikingheterogeneities at cellular level. This variability is particularly well illustrated in polyclonal tumors which constantly undergo mutations. In this respect, single cell analysis is necessary to fully capture the complexity of such tissue. However, working at cellular scale equally exposes many variations in gene expression: from specific biomarkers to insignificant delays in gene expression. High throughput analysis is then needed to multiply the number of profiled cells and discriminate relevant biomarkers from intrinsic population noise.

Droplet microfluidics is particularly well suited and extensively used for high throughput single cell analysis: individual cells are isolated and confined at high speed in pico-volumes to analyze biological processes at the cellular level.


High monodispersity: unique liquid-handling capabilities of microfluidic systems

Reduced costs: volume down scaling from µL to pL compared to pipetting robots

Time saving: molecular diffusion length reduced in small volumes

Higher sensitivity: smaller molecular quantity (1.106-fold less) required to reach minimum detectable concentration

High throughput: up to 1.106 cells compartmentalized per second.


Single cell genomic or transcriptomic analysis: smaller molecular quantity required for detection? reduction of bias related to molecular content amplification

Tissue analysis: investigate cell to cell heterogeneity (polyclonal tumor)

Lineage tracing: enables genomic and biochemical analysis ? more flexible than classical FACS sorting. (Stem cell lineage selection for stem cell therapy)

Cell sorting: smaller number of cells required compared to cytometry ? better adapted to rare samples.

Personalized medicine: single cell analysis of tumor’s heterogeneity associated with selection and amplification of specific corresponding T cells for personalized cancer immunotherapy.

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Selected publications from our customers:

Lu, H. et al. High throughput single cell counting in droplet-based microfluidics. Sci. Rep.2017. 7(1) : 1366

Beneyton T et al, Droplet-based microfluidic high-throughput screening of heterologous enzymes secreted by the yeast Yarrowia lipolytica. Microb Cell Fact. 2017;16(1):18.

Sung YJ et al, Microdroplet photobioreactor for the photoautotrophic culture of microalgal cells. Analyst. 2016 Feb 7;141(3):989-98.

Mary P et al, Analysis of gene expression at the single-cell level using microdroplet-based microfluidic technology. Biomicrofluidics. 2011 Jun;5(2):24109.

Marcoux P.R., et al, Micro-confinement of bacteria into w/o emulsion droplets for rapid detection and enumeration, Colloids and Surfaces A: Physicochem. Eng. Aspects. 2011 ; 377, 54–62

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