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Gene expression analysis of individual cells enables characterization of heterogeneous and rare cell populations, yet widespread implementation of existing single-cell gene analysis techniques has been hindered due to limitations in scale, ease, and cost. Here, we present a novel microdroplet-based, one-step reverse-transcriptase polymerase chain reaction (RT-PCR) platform and demonstrate the detection of three targets simultaneously in over 100,000 single cells in a single experiment with a rapid read-out. Our customized reagent cocktail incorporates the bacteriophage T7 gene 2.5 protein to overcome cell lysate-mediated inhibition and allows for one-step RT-PCR of single cells encapsulated in nanoliter droplets. Fluorescent signals indicative of gene expressions are analyzed using a probabilistic deconvolution method to account for ambient RNA and cell doublets and produce single-cell gene signature profiles, as well as predict cell frequencies within heterogeneous samples. We also developed a simulation model to guide experimental design and optimize the accuracy and precision of the assay. Using mixtures of in vitro transcripts and murine cell lines, we demonstrated the detection of single RNA molecules and rare cell populations at a frequency of 0.1%. This low cost, sensitive, and adaptable technique will provide an accessible platform for high throughput single-cell analysis and enable a wide range of research and clinical applications. [ABSTRACT FROM AUTHOR]

Flow of soft matter objects through one-dimensional environments is important in industrial, biological and biomedical systems. Establishing the underlying principles of the behavior of soft matter in confinement can shed light on its performance in many man-made and biological systems. Here, we report an experimental and theoretical study of translocation of micrometer-size hydrogels (microgels) through microfluidic channels with a diameter smaller than an unperturbed microgel size. For microgels with different dimensions and mechanical properties, under a range of applied pressures, we established the universal principles of microgel entrance and passage through microchannels with different geometries, as well as the reduction in microgel volume in confinement. We also show a non-monotonic change in the flow rate of liquid through the constrained microgel, governed by its progressive confinement. The experimental results were in agreement with the theory developed for non-linear biaxial deformation of unentangled polymer gels. Our work has implications for a broad range of phenomena, including occlusion of blood vessels by thrombi and needle-assisted hydrogel injection in tissue engineering. [ABSTRACT FROM AUTHOR]