SPELL - Nematode

Citation	Von Stetina SE, Watson JD, Fox RM, Olszewski KL, Spencer WC, Roy PJ, Miller DM. Cell-specific microarray profiling experiments reveal a comprehensive picture of gene expression in the C. elegans nervous system. Genome Biol, 2007.
PubMed ID	17612406
Short Description	Cell-specific microarray profiling experiments reveal a comprehensive picture of gene expression in the C. elegans nervous system. GEO Record: GSE8004 Platform: GPL200 Download gene-centric, log2 transformed data: WBPaper00030839.ce.mr.csv
# of Conditions	24
Full Description	ABSTRACT: BACKGROUND: With its fully sequenced genome and simple, well-defined nervous system, the nematode C. elegans offers a unique opportunity to correlate gene expression with neuronal differentiation. The lineal origin, cellular morphology and synaptic connectivity of each of the 302 neurons are known. In many instances, specific behaviors can be attributed to particular neurons or circuits. Here we describe microarray-based methods that monitor gene expression in C. elegans neurons and thereby link comprehensive profiles of neuronal transcription to key developmental and functional properties of the nervous system. RESULTS: We employed complementary microarray-based strategies to profile gene expression in the embryonic and larval nervous systems. In the MAPCeL (Microarray Profiling C. elegans cells) method, we used Fluorescence Activated Cell Sorting (FACS) to isolate GFP-tagged embryonic neurons for microarray analysis. To profile the larval nervous system, we used the mRNA-tagging technique in which an epitope-labeled mRNA binding protein (FLAG-PAB-1) was transgenically expressed in neurons for immunoprecipitation of cell-specific transcripts. These combined approaches identified approximately 2,500 mRNAs that are highly enriched in either the embryonic or larval C. elegans nervous system. These data are validated in part by the detection of gene classes (e.g. transcription factors, ion channels, synaptic vesicle components) with established roles in neuronal development or function. Of particular interest are 19 conserved transcripts of unknown function that are also expressed in the mammalian brain. In addition to utilizing these profiling approaches to define stage-specific gene expression, we also applied the mRNA-tagging method to fingerprint a specific neuron type, the A-class group of cholinergic motor neurons, during early larval development. A comparison of these data to a MAPCeL profile of Embryonic A-class motor neurons identified genes with common functions in both types of A-class motor neurons as well as transcripts with roles specific to each motor neuron type. Conclusion: We describe microarray-based strategies for generating expression profiles of embryonic and larval C. elegans neurons. These methods can be applied to particular neurons at specific developmental stages and therefore provide an unprecedented opportunity to obtain spatially and temporally defined snapshots of gene expression in a simple model nervous system. Experimental Details: WBPaper00030839:Embryonic_Reference_Rep1_Set1 WBPaper00030839:Embryonic_Reference_Rep2_Set1 WBPaper00030839:Embryonic_Reference_Rep3_Set1 WBPaper00030839:Embryonic_Reference_Rep4_Set1 WBPaper00030839:Embryonic_Pan-neural_Rep1_Set1 WBPaper00030839:Embryonic_Pan-neural_Rep2_Set1 WBPaper00030839:Embryonic_Pan-neural_Rep3_Set1 WBPaper00030839:Larval_Reference_Rep1_Set1 WBPaper00030839:Larval_Reference_Rep2_Set1 WBPaper00030839:Larval_Reference_Rep3_Set1 WBPaper00030839:Larval_Reference_Rep4_Set2 WBPaper00030839:Larval_Reference_Rep5_Set2 WBPaper00030839:Larval_Pan-neural_Rep1_Set2 WBPaper00030839:Larval_Pan-neural_Rep2_Set2 WBPaper00030839:Larval_Pan-neural_Rep3_Set2 WBPaper00030839:Larval_A-class_Rep1_Set3 WBPaper00030839:Larval_A-class_Rep2_Set3 WBPaper00030839:Larval_A-class_Rep3_Set3 WBPaper00030839:Larval_A-class_Rep4_Set3 WBPaper00030839:Larval_Reference_Rep1_Set3 WBPaper00030839:Larval_Reference_Rep2_Set3 WBPaper00030839:Larval_Reference_Rep3_Set3 WBPaper00030839:Larval_Reference_Rep4_Set3 WBPaper00030839:Larval_Reference_Rep5_Set3.
Tags	Method: microarray, Species: Caenorhabditis elegans, Tissue Specific: neuron