Additional file 1: Table S1. of Cross-phenotype association tests uncover genes mediating nutrient response in Drosophila
Creators: name: Nelson, Christopher
name: Beck, Jennifer
name: Wilson, Kenneth
name: Pilcher, Elijah
name: Kapahi, Pankaj
name: Brem, Rachel
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: Pharmacology
subject: Developmental Biology
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: FOS: Health sciences
subject: Computational Biology

description: Correlation between phenotypes in DGRP lines raised on two different diets. Table S2. Broad-sense heritabilities of metabolic traits. Table S3. GO terms enriched for association signal in scans of variants with allele frequency ≥5 %. Table S4. Phenotype pairs tested via SMAT. Table S5. GO terms enriched for association signal in scans of variants with allele frequency ≥25 %. Table S6. Strains and crosses used. Figure S1. Variation in metabolic traits and nutrient response across the DGRP. In a given bar chart, each bar reports the mean of the indicated phenotype in an isogenic population of one DGRP line reared on the indicated diet. Strains are ordered along the x-axis by AL diet phenotype. The right hand panels report the same data formatted as a scatterplot. (A), Resistance to acute starvation after rearing adults for 10 days on the indicated diet. (B), Body mass. (C), Whole body triglyceride (TG) content, normalized by body mass. (D), Whole body glucose content, normalized by body mass. a.u., dimensionless arbitrary units. AL, ad libitum diet; DR, dietary restriction. Figure S2. Decreased expression of schlank, htt, hwt, and rdgA upon RNAi. In the first, second, fourth, and sixth panels, each bar reports qRT-PCR measurements of expression of the indicated gene, in a line reared on the indicated diet and harboring both the GeneSwitch (GS) activator and a construct for RNAi of the indicated gene under the control of the indicated driver (da, daughterless; elav, embryonic lethal, abnormal vision), treated with the GS inducer RU486 (+) or a vehicle control (-); in a given diet, each expression measurement is normalized to that from the respective control-treated animals. In the third and fifth panels, each bar reports qRT-PCR measurements of expression of the indicated gene in a strain expressing an RNAi construct for the indicated gene regulated by GAL4 under the daughterless promoter (RNAi) or a background-matched control (Ctrl) with no RNAi construct; in a given diet, each expression measurement is normalized to that from the respective control animals. Figure S3. The GeneSwitch inducer RU486 has no effect on starvation resistance or body mass. (A), Each trace reports survival of flies expressing daughterless promoter (da)-driven GAL4-Gene Switch (GS) that do not harbor an RNAi construct, with drug treatment (dotted lines) or ethanol vehicle treatment (solid lines) starting from eclosion (n = 2 biological replicates of 100 flies per condition). (B), Each column reports the distribution of body mass per fly of the no-RNAi control strain harboring the da-GS driver, with genotypes and treatments as in (A) (n = 2 populations of 15 flies per condition). The checkered boxes indicate addition of the RU486 inducer drug. Top, middle, and bottom horizontal bars of a given vertical box denote the respective quartiles across batches and technical replicates, and the top and bottom short horizontal bars report minimum and maximum, respectively. No changes here were significant by t-test at alpha = 0.05. AL, ad libitum diet; DR, dietary restriction. For strain details see Additional file 1: Table S6. Figure S4. The GeneSwitch inducer RU486 has no effect on triglyceride levels in the absence of an RNAi construct, and htt and hwt knockdown does not detectably impact triglycerides. (A), Each bar reports whole-body triglyceride levels in a strain expressing a ubiquitous da-GeneSwitch driver and no RNAi transgene, treated with the GeneSwitch inducer RU486 (“+ drug”) or with ethanol alone (“- drug”). (B) and (C), Each bar reports whole-body triglyceride levels in a strain expressing constitutive da-GAL4 either with an RNAi construct for the indicated gene (“RNAi”) or without any RNAi construct for the indicated gene (“control”) (n = 1 population of 15 flies per condition). For strain details see Additional file 1: Table S6. AL, animals reared on the ad libitum diet; DR, dietary restriction. Horizontal lines in each boxplot indicate quartiles across technical replicates, and the top and bottom short horizontal bars report minimum and maximum, respectively. No changes here were significant by t-test at alpha = 0.05. Figure S5. Lifespan effects of schlank, htt, hwt and rdgA knockdown. In each panel, the right-hand plot reports survival of flies harboring an RNAi construct for one gene regulated by Act5C-driven GAL4-GeneSwitch treated with the GeneSwitch inducer RU486 (“+ drug”) or with ethanol alone (“no drug”), and the left-hand plot is for a background-matched control without an RNAi transgene. Drug or vehicle treatment was started at eclosion. (A), schlank RNAi. (B), htt RNAi. (C), hwt RNAi. (D), rdgA RNAi. AL, ad libitum diet; DR, dietary restriction. *, p