Genetic analysis of single cells

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A fundamental and unmet challenge in biological research is the need to understand and measure the genome and transcriptional state of individual cells. For instance, nearly all microorganisms on the planet have not been cultivated and may very well be refractory to culture in laboratory settings due to requisite symbiotic relationships with other organisms. Thus, these life forms are not amenable to current technologies for genomic study, which require large numbers and pure populations of cells. On the other hand, even genetically identical cells, such as those in the human body, exhibit widespread heterogeneity owing to differentiation state, stochastic variations, and disease. Scalable single cell analysis technologies are urgently needed and will have far reaching impact touching diverse fields including microbial diversity, cancer biology, and human development. Although advances in instrumentation and chemistries for global sequencing and sensitive targeted measurements of transcription are now available, these are limited by difficulties in manipulating single cells and inefficiencies arising from conventional large-volume (µL) sample processing. Here we will couple the power of these established technologies with new engineering methods for the fabrication of highly integrated "lab-on-a-chip" devices to develop microsystems capable of processing hundreds to thousands of single cells with improved sensitivity and speed. Specifically, we will develop two technologies for i) the high-throughput isolation and genome amplification of uncultivated microbes derived from environmental samples, and ii) the scalable analysis of miRNA expression in mammalian cells.