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Series GSE77905 Query DataSets for GSE77905
Status Public on Feb 16, 2016
Title Natural Genetic Variation Influences Protein Abundances in C. elegans Developmental Signalling Pathways
Organism Caenorhabditis elegans
Experiment type Expression profiling by array
Summary Complex traits, including common disease-related traits, are affected by many different genes that function in multiple pathways and networks. The apoptosis, MAPK, Notch and Wnt signalling pathways play important roles in development and disease progression. At the moment we have a poor understanding of how allelic variation affects gene expression in these pathways at the level of translation. Here we report the effect of natural genetic variation on transcript and protein abundance involved in developmental signalling pathways in Caenorhabditis elegans. We used selected reaction monitoring to analyse proteins from the abovementioned four pathways in a set of recombinant inbred lines (RILs) generated from the wild-type strains Bristol N2 and Hawaii CB4856 to enable quantitative trait loci (QTL) mapping. Variation in gene expression was greater in the RILs than in the parental lines, at the proteome as well as at the transcriptome levels. We detected a trans-QTL on the left arm of chromosome II that affected protein abundance of the phosphatidylserine receptor protein PSR-1, and two separate QTLs that influenced embryonic and ionizing radiation-induced apoptosis on chromosome IV. Our results demonstrate that natural variation in C. elegans is sufficient to cause significant changes in signalling pathways both at the gene expression (transcript and protein abundance) and phenotypic levels.
 
Overall design Parental genotypes N2 (3x) and CB4856 (3x) and 47 RILs from (Li etal 2006; Vinuela etal 2010 and Elvin etal 2011)
 
Contributor(s) Singh K, Roschitzki B, Snoek BL, Grossmann J, Zheng X, Elvin M, Kamkina P, Schrimpf SP, Poulin GB, Kammenga JE, Hengartner MO
Citation(s) 26985669
Submission date Feb 13, 2016
Last update date Mar 21, 2016
Contact name Basten Snoek
E-mail(s) snoek.basten@gmail.com
Organization name Utrecht University
Department Mol. Plant. Physiology
Lab van Zanten
Street address Padualaan
City Utrecht
ZIP/Postal code 3584CH
Country Netherlands
 
Platforms (1)
GPL10094 Agilent-020186 C. elegans (V2) Gene Expression Microarray (Feature Number version)
Samples (78)
GSM2061172 wn190 Array01_Cy3
GSM2061173 wn124 Array02_Cy3
GSM2061174 wn116 Array03_Cy3
Relations
BioProject PRJNA311992

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE77905_RAW.tar 1.1 Gb (http)(custom) TAR (of TXT)
Raw data provided as supplementary file
Processed data included within Sample table

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