Comment[ArrayExpressAccession] E-GEOD-49307 MAGE-TAB Version 1.1 Public Release Date 2013-07-30 Investigation Title A variant in the neuropeptide receptor npr-1 is a major determinant of Caenorhabditis elegans growth and physiology Comment[Submitted Name] A variant in the neuropeptide receptor npr-1 is a major determinant of Caenorhabditis elegans growth and physiology Experiment Description The mechanistic basis for how genetic variants cause differences in phenotypic traits is often elusive. We identified a quantitative trait locus in C. elegans that affects three seemingly unrelated phenotypic traits: lifetime fecundity, adult body size, and susceptibility to the human pathogen Staphyloccus aureus. We found a QTL for all three traits arises from variation in the neuropeptide receptor gene npr-1. Moreover, we found that variation in npr-1 is also responsive for differences in 247 gene expression traits. Variation in npr-1 is known to determine whether animals disperse throughout a bacterial lawn or aggregate at the edges of the lawn. We found that the allele that leads to aggregation is associated with reduced growth and reproductive output. The altered gene expression pattern caused by this allele suggests that the aggregation behavior might cause a weak starvation state, which is known to reduce growth rate and fecundity. Importantly, we show that variation in npr-1 causes each of these phenotypic differences through behavioral avoidance of ambient oxygen concentrations. These results suggest that variation in npr-1 has broad pleiotropic effects mediated by altered exposure to bacterial food. Two-channel experiment comparing mixed stage sample to mixed stage mixed 50:50 N2,CB4856 common reference Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Kruglyak Andersen Bloom Kruglyak Person First Name Leonid Erik Joshua Leonid Person Mid Initials C S Person Email geo@ncbi.nlm.nih.gov Person Affiliation Princeton University Person Address Princeton University, 110 Carl Ichan Laboratory, Princeton, NJ, USA Person Roles submitter Protocol Name P-GSE49307-1 P-GSE49307-3 P-GSE49307-4 P-GSE49307-2 P-GSE49307-5 Protocol Description Median signal processed in R using limma, background corrected, within array loess normalization, and Gquantile between array normalization, replicate probes averaged ID_REF = VALUE = log2(Cy5/Cy3) RNA was labeled using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent, San Jose CA) according to the manufacturer's instructions Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential Total RNA extracted using Trizol following manufacturer's instructions Scanned on an Agilent G2505B Scanner Protocol Type normalization data transformation protocol labelling protocol hybridization protocol nucleic acid extraction protocol array scanning protocol Experimental Factor Name STRAIN OR LINE GENETIC BACKGROUND/NPR-1 ALLELE Experimental Factor Type strain or line genetic background/npr-1 allele Comment[SecondaryAccession] GSE49307 Comment[GEOReleaseDate] 2013-07-30 Comment[ArrayExpressSubmissionDate] 2013-07-29 Comment[GEOLastUpdateDate] 2013-07-30 Comment[AEExperimentType] transcription profiling by array SDRF File E-GEOD-49307.sdrf.txt