E-GEOD-8462 - Transcription profiling of C. elegans embryonic muscle

Status
Submitted on 12 July 2007, released on 16 June 2008, last updated on 27 March 2012
Organism
Caenorhabditis elegans
Samples (13)
Array (1)
Protocols (6)
Description
Background: The force generating mechanism of muscle is evolutionarily ancient; the fundamental structural and functional components of the sarcomere are common to motile animals throughout phylogeny. Recent evidence suggests that the transcription factors that regulate muscle development are also conserved. Thus, a comprehensive description of muscle gene expression in a simple model organism should define a basic muscle transcriptome that is also expressed in animals with more complex body plans. To this end, we have applied Micro-Array Profiling of Caenorhabditis elegans Cells (MAPCeL) to muscle cell populations extracted from developing Caenorhabditis elegans embryos. Results: Fluorescence Activated Cell Sorting (FACS) was used to isolate myo-3::GFP-positive muscle cells, and their cultured derivatives, from dissociated early Caenorhabditis elegans embryos. Microarray analysis identified 6,693 expressed genes, 1,305 of which are enriched in the myo-3::GFP positive cell population relative to the average embryonic cell. The muscle-enriched gene set was validated by comparisons to known muscle markers, independently derived expression data, and GFP reporters in transgenic strains. These results confirm the utility of MAPCeL for cell type-specific expression profiling and reveal that 60% of these transcripts have human homologs. Conclusions: This study provides a comprehensive description of gene expression in developing Caenorhabditis elegans embryonic muscle cells. The finding that over half of these muscle-enriched transcripts encode proteins with human homologs suggests that mutant analysis of these genes in Caenorhabditis elegans could reveal evolutionarily conserved models of muscle gene function with ready application to human muscle pathologies. Experiment Overall Design: Our goal is to profile gene expression in the major excitable tissues of Caenorhabditis elegans. As part of this effort, we profiled embryonic muscle cells at two timepoints: 0hr and 24hr.. To isolate transcripts from these cells we utilized the MAPCeL (Microarray Profiling Caenorhabditis elegans Cells) technique, which our lab previously developed (Fox et al 2005) in which myo-3::GFP+ cells are captured by FACS for RNA isolation. We verified these data by bioinformatic means and by in vivo validation by creating GFP reporters for a random set of genes in our enriched gene list.
Experiment types
transcription profiling by array, unknown experiment type
Contact
Citation
The embryonic muscle transcriptome of Caenorhabditis elegans. Rebecca M Fox, Joseph D Watson, Stephen E Von Stetina, Joan McDermott, Thomas M Brodigan, Tetsunari Fukushige, Michael Krause, David M Miller. Genome Biol 8(9):R188 (2007)
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-8462.idf.txt
Sample and data relationshipE-GEOD-8462.sdrf.txt
Raw data (1)E-GEOD-8462.raw.1.zip
Processed data (1)E-GEOD-8462.processed.1.zip
Array designA-AFFY-60.adf.txt
R ExpressionSetE-GEOD-8462.eSet.r
Links