Isolation of specific neurons from C. elegans larvae for gene expression profiling.
BACKGROUND
The simple and well-described structure of the C. elegans nervous system offers an unprecedented opportunity to identify the genetic programs that define the connectivity and function of individual neurons and their circuits. A correspondingly precise gene expression map of C. elegans neurons would facilitate the application of genetic methods toward this goal. Here we describe a powerful new approach, SeqCeL (RNA-Seq of C. elegans cells) for producing gene expression profiles of specific larval C. elegans neurons.


RESULTS
We have exploited available GFP reporter lines for FACS isolation of specific larval C. elegans neurons for RNA-Seq analysis. Our analysis showed that diverse classes of neurons are accessible to this approach. To demonstrate the applicability of this strategy to rare neuron types, we generated RNA-Seq profiles of the NSM serotonergic neurons that occur as a single bilateral pair of cells in the C. elegans pharynx. These data detected >1,000 NSM enriched transcripts, including the majority of previously known NSM-expressed genes.


CONCLUSIONS
This work offers a simple and robust protocol for expression profiling studies of post-embryonic C. elegans neurons and thus provides an important new method for identifying candidate genes for key roles in neuron-specific development and function.
Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, United States of America.
W Clay
WC
Spencer
Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, United States of America.
Rebecca
R
McWhirter
Program in Neuroscience, Vanderbilt University, Nashville, Tennessee, United States of America.
Tyne
T
Miller
Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, United States of America.
Pnina
P
Strasbourger
Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, United States of America.
Owen
O
Thompson
Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, United States of America.
LaDeana W
LW
Hillier
Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, United States of America.
Robert H
RH
Waterston
Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, United States of America; Program in Neuroscience, Vanderbilt University, Nashville, Tennessee, United States of America.
David M
DM
Miller
D000818:Animals; D017173:Caenorhabditis elegans / Q000166:cytology / Q000378:metabolism; D002469:Cell Separation / Q000379:methods; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000502:physiology; D009474:Neurons / Q000166:cytology / Q000378:metabolism