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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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RNAi knock down of daf-2, daf-3, daf-16 in C. elegans over 0-48 hours

ABSTRACT: Comparison of sterile worms grown on Control Vector, daf-2 RNAi, and daf-2 + daf-16 RNAi. Synchronized fer-15(b26); fem-1(hc17) animals were grown on RNAi bacteria at 25ºC, induced with IPTG on Day 1 of adulthood, and collected from 0-48 hours (10 time points) and 0-196 hours (10 time points); RNAi bacteria was supplemented as necessary for later time points. Worms were floated off lawns with M9 buffer, centrifuged, and washed again in M9. The pelleted worms were dissolved in Trizol (Gibco) and frozen in liquid nitrogen.Time courses were compared with mixed references (collected from 1/2 of each of the time course samples)

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Coleen Murphy

PROVIDER: E-MEXP-8 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans.

Murphy Coleen T CT McCarroll Steven A SA Bargmann Cornelia I CI Fraser Andrew A Kamath Ravi S RS Ahringer Julie J Li Hao H Kenyon Cynthia C

Nature 20030629 6946

Ageing is a fundamental, unsolved mystery in biology. DAF-16, a FOXO-family transcription factor, influences the rate of ageing of Caenorhabditis elegans in response to insulin/insulin-like growth factor 1 (IGF-I) signalling. Using DNA microarray analysis, we have found that DAF-16 affects expression of a set of genes during early adulthood, the time at which this pathway is known to control ageing. Here we find that many of these genes influence the ageing process. The insulin/IGF-I pathway fun ...[more]

PMID: 12845331

Similar Datasets

RNAi knock down of daf-16 in C. elegans over 0-192 hours

Project description:Comparison of sterile worms grown on Control Vector, daf-2 RNAi, and daf-2 + daf-16 RNAi. Synchronized fer-15(b26); fem-1(hc17) animals were grown on RNAi bacteria at 25ºC, induced with IPTG on Day 1 of adulthood, and collected from 0-48 hours (10 time points) and 0-196 hours (10 time points); RNAi bacteria was supplemented as necessary for later time points. Worms were floated off lawns with M9 buffer, centrifuged, and washed again in M9. The pelleted worms were dissolved in Trizol (Gibco) and frozen in liquid nitrogen.Time courses were compared with mixed references (collected from 1/2 of each of the time course samples)

2003-07-17 | E-MEXP-9 | biostudies-arrayexpress

Transcription profiling of long-lived C.elegans daf-2 pathway mutants with wild type/short-lived mutants

Project description:Comparison of long-lived daf-2 pathway mutants with wild type/short-lived mutants. A: age-1 fer-15; fem-1 vs. fer-15; fem-1. B: age-1 fer-15; fem-1 vs. fer-15; fem-1. C: fer-15; daf-2(mu150); fem-1 vs. fer-15; fem-1. D: fer-15; daf-2(mu150); fem-1 vs. fer-15; fem-1. E: daf-16::gfp in daf-16(mu86);daf-2(e1370) vs. daf-16(mu86);daf-2(e1370). F: daf-2(e1368); fer-15; fem-1 vs. fer-15; fem-1. G: fer-15; daf-2(mu150); fem-1 vs. fer-15; fem-1. H: age-1 fer-15; fem-1 vs. fer-15; fem-1. I: fer-15; daf-2(mu150); fem-1 vs. fer-15; fem-1. J: daf-16::gfp in daf-2(e1370); daf-16(mu86) vs. daf-2(e1370); daf-16(mu86). K: daf-2(mu150) vs. wild type. L: daf-2(e1370) vs. daf-2(e1370); daf-16(mu86). M: daf-2(e1370) vs. daf-2(e1370); daf-16(mu86). N: daf-2(e1370) vs. daf-2(e1370); daf-16(mu86).

2003-07-17 | E-MEXP-7 | biostudies-arrayexpress

RNA-seq analysis comparing gene expression of unc-43(gf), unc-43(-) and egl-8(-) to the corresponding control strain in daf-2(+) and daf-2(-) background

Project description:To identify genes whose expression in Caenorhabditis elegans is regulated by unc-43/CamKII or egl-8/PLCbeta during adulthood, we performed an exploratory whole transcriptome RNA-sequencing (RNA-seq) study on unc-43(gf), unc-43(-), egl-8(-) and corresponding unc-43(+)/egl-8(+) control worms. To further account for potential influences of genetic background on unc-43/egl-8 function, these experiments were conducted in long-lived insulin-receptor defective [daf-2(-)], as well as in otherwise wildtype [i.e daf-2(+)] strains.

2022-10-01 | E-MTAB-11045 | biostudies-arrayexpress

RNA-seq analysis comparing gene expression between mbk-1(-) and mbk-1(+) strains in daf-2(+), daf-2(-), glp-1(+) and glp-1(-) background

Project description:To identify genes whose expression in Caenorhabditis elegans is regulated by mbk-1 (ortholog of the human protein kinase DYRK1A implicated in Down syndrome) during adulthood, we performed whole transcriptome RNA-sequencing (RNA-seq) on mbk-1(+) and mbk-1(-) worms. To further account for the influence of genetic background on mbk-1 function, these experiments were conducted in long-lived insulin-receptor defective [daf-2(-)] or germline stem cell [GSC] deficient [glp-1(-), i.e. GSC(-)] strains, as well as in corresponding [i.e daf-2(+) or glp-1(+)/GSC(+)] control strains.

2021-11-25 | E-MTAB-10898 | biostudies-arrayexpress

wt vs daf-2 C. elegans protein turnover

Project description:Most aging hypotheses revolve around the accumulation of some sort of damage resulting in gradual physiological decline and ultimately death. Avoiding protein damage accumulation by enhanced turnover should slow down the aging process and extend lifespan. However, lowering translational efficiency extends rather than shortens lifespan in C. elegans. We studied turnover of individual proteins in the conserved Insulin/Insulin-like Growth Factor (IGF-1) receptor mutant daf-2 by combining Stable Isotope Labeling by Nitrogen-15 in Caenorhabditis elegans and LC-MS/MS. Intriguingly, the majority of proteins displayed prolonged half-lives in daf-2, while others remained unchanged, signifying that longevity is not supported by high protein turnover. This slow-down of protein turnover was most prominent for components of the translation machinery and mitochondria. In contrast, the high turnover of lysosomal hydrolases and very low turnover of cytoskeletal proteins remained largely unchanged in daf-2. The slow-down of protein dynamics and decreased abundance of the translational machinery may point at the importance of anabolic attenuation in lifespan extension as suggested by the hyperfunction theory.

2016-09-27 | PXD002317 | Pride

Identification of transcription factor DAF-16 binding sites in C. elegans

Project description:We identified the DNA binding sites of DAF-16 in transgenic line TJ356 (daf-16::gfp) that carries high-copy number daf-16. The expression pattern was examined through fluorescent microscopy. The binding sites were determined using chromatin immunoprecipitation with anti-GFP antibody and anti-POL II antibody followed by illumina high-throughput sequencing (ChIP-seq). For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Identification of DAF-16 binding sites at L4/Young adult stage when DAF-16 was highly overexpressed

2009-04-11 | E-GEOD-15567 | biostudies-arrayexpress

daf-16/FoxO isoform-specific deletion mutants

Project description:FoxO transcription factors promote longevity across taxa. How they do so is poorly understood. In the nematode Caenorhabditis elegans, the A- and F-isoforms of the FoxO transcription factor DAF-16 extend life span in the context of reduced DAF-2 insulin-like growth factor receptor (IGFR) signaling. To elucidate the mechanistic basis for DAF-16/FoxO-dependent life span extension, we performed an integrative analysis of isoform-specific daf-16/FoxO mutants. In contrast to previous studies suggesting that DAF-16F plays a more prominent role in life span control than DAF-16A, isoform-specific daf-16/FoxO mutant phenotypes and whole transcriptome profiling revealed a predominant role for DAF-16A over DAF-16F in life span control, stress resistance, and target gene regulation. Integration of these data sets enabled the prioritization of a subset of 92 DAF-16/FoxO target genes for functional interrogation. Among 29 genes tested, two DAF-16A-specific target genes significantly influenced longevity. Our discovery of new longevity genes underscores the efficacy of our integrative strategy while providing a general framework for identifying specific downstream gene regulatory events that contribute substantially to transcription factor functions. As FoxO transcription factors have conserved functions in promoting longevity and may be dysregulated in aging-related diseases, these findings promise to illuminate fundamental principles underlying aging in animals. Whole-transcriptome profiling of daf-16/FoxO isoform-specific deletion mutants in the long-lived daf-2(e1370) background. Included are daf-16 wild-type, daf-16 null mutation, daf-16a/f mutation, two independent daf-16a mutations, and daf-16f mutation. N2 wild-type controls are also included.

2015-08-27 | E-GEOD-72426 | biostudies-arrayexpress

Adult C. elegans: Control daf-2 mutants treated with daf-16 RNAi vs. daf-2 mutants treated with empty vector RNAi

Project description:Transcriptional profiling of adult C. elegans comparing daf-16(-); daf-2(-) animals with adult daf-2(-) animals. Two-condition experiment, daf-2 mutants treated with daf-16 RNAi vs. daf-2 mutants treated with empty vector RNAi. Biological replicates: 8 daf-2 mutants treated with daf-16 RNAi vs. daf-2 mutants treated with empty vector RNAi, independently grown and harvested. One replicate per array.

2010-05-16 | E-GEOD-18561 | biostudies-arrayexpress

Defining changes in the total levels of proteins during aging of C. elegans

Project description:We performed label-free proteomics in C. elegans to define and quantify changes in the ubiquitinated (Ub)-proteome during the aging process. More specifically, we compared wild-type worms at the first day of adulthood with young (day 5), mid-age (day 10) and aged adults (day 15). Moreover, we assessed protein levels of age-matched long-lived genetic models of dietary restriction (eat-2(ad1116)) and reduced insulin/IGF-1 signaling (daf-2(e1370)).

2021-05-26 | PXD025128 | Pride

Endogenous DAF-16 genome-wide recruitment under low Insulin signalling condition in Caenorhabditis elegans

Project description:In order to understand the complexity of gene regulation downstream of IIS, we did RNA-seq in mixed culture in wild-type, daf-2(e1370), daf-16(mgDf50);daf-2(e1370) and daf-2(e1370);daf-12(m20 and correlated it with ChIP-seq data RNA-seq profile of different mutants in mix stage

2016-03-01 | E-GEOD-67975 | biostudies-arrayexpress

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