{
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"PROJECT":{"PROJECT_TITLE":"Natural genetic variation in C. elegans identified genomic loci controlling metabolite levels","PROJECT_TYPE":"Targeted metabolomics analysis","PROJECT_SUMMARY":"Metabolic homeostasis is sustained by complex biological networks that respond to nutrient availability. Genetic and environmental factors may disrupt this equilibrium leading to metabolic disorders, including obesity and type 2 diabetes. To identify the genetic factors controlling metabolism, we performed quantitative genetic analysis using a population of 199 recombinant inbred lines (RILs) in the nematode Caenorhabditis elegans. We focused on the genomic regions that control metabolite levels by measuring fatty acid (FA) and amino acid (AA) composition in the RILs using targeted metabolomics. The genetically diverse RILs showed a large variation in their FA and AA levels with a heritability ranging from 32-82%. We detected strongly co-correlated metabolite clusters and 36 significant metabolite QTL (mQTL). We focused on mQTL displaying highly significant linkage and heritability, including an mQTL for the FA C14:1 on Chromosome I, and another mQTL for the FA C18:2 on Chromosome IV. Using introgression lines (ILs) we were able to narrow down both mQTL to a 1.4 Mbp and a 3.6 Mbp region, respectively. RNAi-based screening focusing on the Chromosome I mQTL identified several candidate genes for the C14:1 mQTL, including lagr-1, Y87G2A.2, nhr-265, nhr-276, and nhr-81. Overall, this systems approach provides us with a powerful platform to study the genetic basis of C. elegans metabolism. Furthermore, it allows us to investigate interventions, such as nutrients and stresses that maintain or disturb the regulatory network controlling metabolic homeostasis, and identify gene-by-environment interactions.","INSTITUTE":"Academic Medical Center of Amsterdam","LAST_NAME":"Gao","FIRST_NAME":"Arwen","ADDRESS":"Meibergdreef 9, Amsterdam, North-Holland, 1105 AZ, Netherlands","EMAIL":"w.gao@amc.nl","PHONE":"0031205663827"},

"STUDY":{"STUDY_TITLE":"Natural genetic variation in C. elegans identified genomic loci controlling metabolite levels","STUDY_TYPE":"Metabolomics in C. elegans","STUDY_SUMMARY":"Metabolic homeostasis is sustained by complex biological networks that respond to nutrient availability. Genetic and environmental factors may disrupt this equilibrium leading to metabolic disorders, including obesity and type 2 diabetes. To identify the genetic factors controlling metabolism, we performed quantitative genetic analysis using a population of 199 recombinant inbred lines (RILs) in the nematode Caenorhabditis elegans. We focused on the genomic regions that control metabolite levels by measuring fatty acid (FA) and amino acid (AA) composition in the RILs using targeted metabolomics. The genetically diverse RILs showed a large variation in their FA and AA levels with a heritability ranging from 32-82%. We detected strongly co-correlated metabolite clusters and 36 significant metabolite QTL (mQTL). We focused on mQTL displaying highly significant linkage and heritability, including an mQTL for the FA C14:1 on Chromosome I, and another mQTL for the FA C18:2 on Chromosome IV. Using introgression lines (ILs) we were able to narrow down both mQTL to a 1.4 Mbp and a 3.6 Mbp region, respectively. RNAi-based screening focusing on the Chromosome I mQTL identified several candidate genes for the C14:1 mQTL, including lagr-1, Y87G2A.2, nhr-265, nhr-276, and nhr-81. Overall, this systems approach provides us with a powerful platform to study the genetic basis of C. elegans metabolism. Furthermore, it allows us to investigate interventions, such as nutrients and stresses that maintain or disturb the regulatory network controlling metabolic homeostasis, and identify gene-by-environment interactions.","INSTITUTE":"Academic Medical Center of Amsterdam","LAST_NAME":"Gao","FIRST_NAME":"Arwen","ADDRESS":"Meibergdreef 9, Amsterdam, North-Holland, 1105 AZ, Netherlands","EMAIL":"w.gao@amc.nl","PHONE":"0031205663827"},

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{
"Subject ID":"-",
"Sample ID":"WN159_b1_4",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN159_b1_8",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN159_b2_8",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN159_b3_8",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN160_b1_6",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN161_b1_4",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN161_b1_8",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN161_b2_8",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN161_b3_8",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN162_b1_4",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN162_b1_8",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN162_b2_8",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN162_b3_8",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN163_b1_6",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN164_b1_6",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN165_b1_6",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN166_b1_6",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN167_b1_6",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN168_b1_6",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN169_b1_6",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN170_b1_6",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN171_b1_4",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN171_b1_8",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN171_b2_8",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN171_b3_8",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN172_b1_6",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN173_b1_6",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN174_b1_4",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN174_b1_8",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN174_b2_8",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN174_b3_8",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN175_b1_6",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN176_b1_4",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN176_b1_8",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN176_b2_8",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN176_b3_8",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN177_b1_4",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN177_b1_8",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN177_b2_8",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN177_b3_8",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN178_b1_6",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN178_b1_7",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN179_b1_6",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN179_b1_7",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN180_b1_6",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN181_b1_6",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN182_b1_6",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN183_b1_6",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN184_b1_6",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN185_b1_4",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN185_b1_8",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN185_b2_8",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN185_b3_8",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN186_b1_4",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN186_b1_7",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN186_b1_8",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN186_b2_8",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN186_b3_8",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN187_b1_6",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN188_b1_6",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN189_b1_6",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN190_b1_6",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN190_b1_7",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN190_b1_8",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN190_b2_8",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN190_b3_8",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN191_b1_6",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN192_b1_6",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN193_b1_6",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN194_b1_6",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN194_b1_7",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN195_b1_4",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN195_b1_8",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN195_b2_8",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN195_b3_8",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN196_b1_6",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN197_b1_6",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN197_b1_7",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN198_b1_6",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN199_b1_6",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN200_b1_6",
"Factors":{"Strain type":"RIL strain"}
},
{
"Subject ID":"-",
"Sample ID":"WN212_b1_9",
"Factors":{"Strain type":"Introgression line"}
},
{
"Subject ID":"-",
"Sample ID":"WN212_b2_9",
"Factors":{"Strain type":"Introgression line"}
},
{
"Subject ID":"-",
"Sample ID":"WN212_b3_9",
"Factors":{"Strain type":"Introgression line"}
},
{
"Subject ID":"-",
"Sample ID":"WN212_b4_9",
"Factors":{"Strain type":"Introgression line"}
},
{
"Subject ID":"-",
"Sample ID":"WN215_b1_9",
"Factors":{"Strain type":"Introgression line"}
},
{
"Subject ID":"-",
"Sample ID":"WN215_b2_9",
"Factors":{"Strain type":"Introgression line"}
},
{
"Subject ID":"-",
"Sample ID":"WN215_b3_9",
"Factors":{"Strain type":"Introgression line"}
},
{
"Subject ID":"-",
"Sample ID":"WN215_b4_9",
"Factors":{"Strain type":"Introgression line"}
},
{
"Subject ID":"-",
"Sample ID":"WN217_b1_9",
"Factors":{"Strain type":"Introgression line"}
},
{
"Subject ID":"-",
"Sample ID":"WN217_b2_9",
"Factors":{"Strain type":"Introgression line"}
},
{
"Subject ID":"-",
"Sample ID":"WN217_b3_9",
"Factors":{"Strain type":"Introgression line"}
},
{
"Subject ID":"-",
"Sample ID":"WN217_b4_9",
"Factors":{"Strain type":"Introgression line"}
},
{
"Subject ID":"-",
"Sample ID":"WN218_b1_9",
"Factors":{"Strain type":"Introgression line"}
},
{
"Subject ID":"-",
"Sample ID":"WN218_b2_9",
"Factors":{"Strain type":"Introgression line"}
},
{
"Subject ID":"-",
"Sample ID":"WN218_b3_9",
"Factors":{"Strain type":"Introgression line"}
},
{
"Subject ID":"-",
"Sample ID":"WN218_b4_9",
"Factors":{"Strain type":"Introgression line"}
},
{
"Subject ID":"-",
"Sample ID":"WN251_b1_9",
"Factors":{"Strain type":"Introgression line"}
},
{
"Subject ID":"-",
"Sample ID":"WN251_b2_9",
"Factors":{"Strain type":"Introgression line"}
},
{
"Subject ID":"-",
"Sample ID":"WN251_b3_9",
"Factors":{"Strain type":"Introgression line"}
},
{
"Subject ID":"-",
"Sample ID":"WN251_b4_9",
"Factors":{"Strain type":"Introgression line"}
},
{
"Subject ID":"-",
"Sample ID":"WN252_b1_9",
"Factors":{"Strain type":"Introgression line"}
},
{
"Subject ID":"-",
"Sample ID":"WN252_b2_9",
"Factors":{"Strain type":"Introgression line"}
},
{
"Subject ID":"-",
"Sample ID":"WN252_b3_9",
"Factors":{"Strain type":"Introgression line"}
},
{
"Subject ID":"-",
"Sample ID":"WN252_b4_9",
"Factors":{"Strain type":"Introgression line"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"A synchronous population of young adult worms was washed off the plates in M9 buffer and the worm pellet was washed with dH2O for three times and then collected in a 2 mL Eppendorf tube and freeze-dried overnight. Dried worm pellets were stored at room temperature until use.","SAMPLE_TYPE":"Worms","STORAGE_CONDITIONS":"Room temperature"},

"TREATMENT":{"TREATMENT_SUMMARY":"Nematodes were cultured and maintained at 20°C on nematode growth media (NGM) agar plates. Culture conditions in all experiments were the same unless indicated otherwise. For metabolite profiling of 199 RIL strains, N2, and CB4856, age synchronized worms were obtained by alkaline hypochlorite treatment of gravid adults grown on E. coli OP50 lawn, 2000 eggs of each strain were then seeded onto NGM plates and cultured for 2.5 days allowing development to young adults."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"A synchronous population of young adult worms was washed off the plates in M9 buffer and the worm pellet was washed with dH2O for three times and then collected in a 2 mL Eppendorf tube and freeze-dried overnight. Dried worm pellets were stored at room temperature until use. A dry worm pellet was re-suspended in ice-cold 0.9% NaCl solution (250 µL). Worms were homogenized with a 5 mm steel bead using a TissueLyser II (Qiagen) for 2x2.5 min at frequency of 30 times/sec, followed by a tip sonication (energy level: 40 joule; output: 8 watts) for two times on ice water. Protein quantification was performed with BCA assay."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"For fatty acids:The MS system consisted of an Acquity UPLC Binary Solvent manager (Waters, Milford MA) and an Acquity UPLC sample manager connected to a Quattro Premier XE mass spectrometer (Waters, Milford MA), used in the negative ESI mode. For amino acids:Liquid chromatography was performed at 50°C using a Acquity UPLC BEH C18, 1.7 µm, 2.1 x 100 mm column (Waters, Milford MA) and the injected volume was 10 µL. Mass spectrometry experiments were performed using a Micromass Quattro Premier XE Tandem Mass Spectrometer (waters, Milford, MA). The mass spectrometer was used in the multiple reaction monitoring mode (MRM) in the ESI-positive mode.","CHROMATOGRAPHY_TYPE":"None (Direct infusion)","INSTRUMENT_NAME":"Waters Acquity","COLUMN_NAME":"none"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"Waters Quattro Premier XE","INSTRUMENT_TYPE":"Triple quadrupole","MS_TYPE":"ESI","ION_MODE":"NEGATIVE"},

"MS_METABOLITE_DATA":{
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