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Fast and high-throughput single-cell analysis with microfluidic chips

Single-cell analysis has become one of the most important applications of microfluidic technology in recent years. It refers to the process of isolation, manipulation, and analysis of the cells at single-cell resolution via microfluidic chips. Depending on the application, single-cell analysis chips can include any or all the above-mentioned steps.

The small size of the cells makes it difficult to conduct single-cell analysis using conventional cell culture methods. Also, conventional methods normally rely upon the bulk analysis of the culture while the cells are primarily heterogenous. Oftentimes, the concentration of the target cells can be very low making it even more challenging to isolate and work with individual cells. Therefore, these conventional techniques come short of capturing the cell-to-cell differences and the heterogeneity of the culture.

Microfluidics is associated with handling and manipulating very tiny amounts of fluids and chemical and biological analytes. Microfluidics for single-cell analysis have gained significant attention lately. Various microfluidic methods have been developed for isolating, manipulating, and analyzing single cells.

Microfluidic approaches for single-cell isolation

Isolation is the first step for working with individual cells. Isolation is the process at which the target cells are separated and isolated to be manipulated or analyzed. Conventionally, it was done using FACS machines that require expensive and bulky equipments as well as trained personnel. Various microfluidic methods have been developed for isolating single cells. It should be noted that it might be needed to first separate two different cell types from each other followed by isolating a specific type. For this, microfluidic cell separation methods should be first employed to separate the desired cell type. Microfluidic single-cell isolation methods include but are not limited to the following:


Here, an array of microwells are required to isolate the cells. The parameters that matter here are the size of the pores and the modification of the surface. The pores allow the single cells to be trapped and released by inverting the flow upon the experiment. The density of the microwells can be quite high in each microfluidic chip. Microchips with ~10000 wells have been made.


Traps include active and passive methods. Passive methods do not require any external power source while active techniques rely on an external source. Among passive approaches, hydrodynamic traps are popular. Two common hydrodynamic traps are U-shaped traps where single cells are trapped inside a U-shaped barrier and bypass channel traps where the cells are sucked into side channels.
Active microfluidic single-cell traps often use electrical or optical sources to capture the cells. Optical tweezers employ a highly focused laser beam to grab a single-cell and transfer it to a desired location.


Droplet microfluidics is indeed the most popular microfluidic method for single-cell analysis. Here, a droplet microfluidic chip is used to generate droplet at kHz frequencies. The droplets will encapsulate single-cells while formation and serve as a bioreactor or a microchamber for the cells. The concentration of the cells is often adjusted using Poisson distribution to ensure the droplets do not contain more than one cell. A variety of microfluidic methods have been developed for post-modification and analysis of these cell encapsulating droplets. For example, the droplets can contain a lysis reagent and barcodes to lyse the cells and sequence the RNA.

Further Reading

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