Single cell transcriptome studies are transforming our knowledge about cell types and cell states, and revealing important variation in gene expression that is otherwise hidden in the context of bulk measurements. Single cell RNA-Seq technology and analysis tools are rapidly evolving, and the complexity of such studies necessitates careful statistical considerations. In this workshop, we provide an overview of the sequencing technologies and experimental methods that make possible single cell transcriptome sequencing. Through hands-on activities with single cell RNA-Seq data, we explore analysis methods available for exploring the variation in transcript expression among cells, define clusters of related cells, and identify characteristics of cell types that are relevant to their biological function.