Single Cell Transcription Profiling to Better Understand Developmental Decisions

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SELECTBIO

Development begins with the fertilized egg, which gives rise to an adult with amazing cellular variety and multiple organ systems. Underlying the enormous complexity of this process are simplifying strategies that make repeated use of individual genes and signaling systems to drive distinct developmental decisions in different contexts. At many stages in development we observe histologically uniform groups of cells that produce varied progeny. We know that morphogen gradients, flanking cell crosstalk, and even stochastic gene expression can regulate decisions that generate diversity from apparent uniformity. Nevertheless, to date we have not created a detailed blueprint of this process, at single cell resolution, for any developing organ system. Studies of population pools cannot define early events marking distinct developmental destinies in flanking cells that appear identical. Single cell analysis is required. To this end we have been using the Fludigm C1 microfluidic/robotic system that facilitates high throughput single cell RNA-Seq gene expression profiling. We have applied this technology to the analysis of lung and kidney development. Many hundreds of single cells were examined with RNA-Seq. The challenges of this approach, including technical and biological noise, will be discussed. This strategy can be applied to the analysis of any system with interesting cellular heterogeneity present.