Isolation of specific neurons from C. elegans larvae for gene expression profiling

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...

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Bibliographic Details
Published in:PloS one 2014-11, Vol.9 (11), p.e112102-e112102
Main Authors: Spencer, W Clay, McWhirter, Rebecca, Miller, Tyne, Strasbourger, Pnina, Thompson, Owen, Hillier, LaDeana W, Waterston, Robert H, Miller, 3rd, David M
Format: Article
Language:English
Subjects:
Analysis
Animals
Bioinformatics
Biology and life sciences
Caenorhabditis elegans
Caenorhabditis elegans - cytology
Caenorhabditis elegans - metabolism
Cell Separation - methods
Computer and Information Sciences
Data processing
Developmental biology
Embryos
Experiments
Flow cytometry
Gene expression
Gene Expression Profiling
Gene Expression Regulation - physiology
Genes
Genetic programs
Genetic research
Genomes
Hypoxia
Larvae
Medical research
Medicine
Nematodes
Nervous system
Neural networks
Neurons
Neurons - cytology
Neurons - metabolism
Neurosciences
Pharynx
Research and Analysis Methods
Ribonucleic acid
RNA
Serotonin
Transcription factors
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Summary: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. 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. 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.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0112102