PT - JOURNAL ARTICLE AU - Seth R Taylor AU - Gabriel Santpere AU - Molly Reilly AU - Lori Glenwinkel AU - Abigail Poff AU - Rebecca McWhirter AU - Chuan Xu AU - Alexis Weinreb AU - Manasa Basavaraju AU - Steven J Cook AU - Alec Barrett AU - Alexander Abrams AU - Berta Vidal AU - Cyril Cros AU - Ibnul Rafi AU - Nenad Sestan AU - Marc Hammarlund AU - Oliver Hobert AU - David M. Miller III TI - Expression profiling of the mature <em>C. elegans</em> nervous system by single-cell RNA-Sequencing AID - 10.1101/737577 DP - 2019 Jan 01 TA - bioRxiv PG - 737577 4099 - http://biorxiv.org/content/early/2019/08/17/737577.short 4100 - http://biorxiv.org/content/early/2019/08/17/737577.full AB - A single neuron and its synapses define the fundamental structural motif of the brain but the underlying gene expression programs that specify individual neuron types are poorly understood. To address this question in a model organism, we have produced a gene expression profile of &gt;90% of the individual neuron classes in the C. elegans nervous system, an ensemble of neurons for which both the anatomy and connectivity are uniquely defined at single cell resolution. We generated single cell transcriptomes for 52,412 neurons that resolve as clusters corresponding to 109 of the canonical 118 neuron classes in the mature hermaphrodite nervous system. Detailed analysis revealed molecular signatures that further subdivide identified classes into specific neuronal subtypes. Notably, neuropeptide-related genes are often differentially expressed between subtypes of the given neuron class which points to distinct functional characteristics. All of these data are publicly available at our website (http://www.cengen.org) and can be interrogated at the web application SCeNGEA (https://cengen.shinyapps.io/SCeNGEA). We expect that this gene expression catalog will spur the goal of delineating the underlying mechanisms that define the developmental lineage, detailed anatomy, synaptic connectivity and function of each type of C. elegans neuron.