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Expression data of wild-type C. elegans shifted from 23 degrees to 17 degrees

ABSTRACT: C. elegans exhibits thermotaxis, where most of the animals that had been cultivated at a particular temperature ranging from 15°C to 25°C for a few hours with a food source and then placed on a thermal gradient for an hour migrate to the cultivation temperature. In addition, animals that were previously conditioned to migrate to a certain temperature are capable of migrating to a new cultivation temperature a few hours after the cultivation temperature was shifted to the new temperature To gain the detailed molecular insight into thermotactic behavior, the genome-wide microarray analysis during behavioral conditioning was performed. We compared the transcriptional profile of animals conditioned to migrate to the new temperature 17°C with that of animals conditioned to migrate to the previous temperature 23°C Synchronized adult wild-type animals cultivated at 23 degrees were selected for RNA extraction and hybridization on Affymetrix microarrays.

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Takuma Sugi

PROVIDER: E-GEOD-28856 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression data of wild-type C. elegans shifted from 23 degrees to 17 degrees

Project description:C. elegans exhibits thermotaxis, where most of the animals that had been cultivated at a particular temperature ranging from 15°C to 25°C for a few hours with a food source and then placed on a thermal gradient for an hour migrate to the cultivation temperature. In addition, animals that were previously conditioned to migrate to a certain temperature are capable of migrating to a new cultivation temperature a few hours after the cultivation temperature was shifted to the new temperature To gain the detailed molecular insight into thermotactic behavior, the genome-wide microarray analysis during behavioral conditioning was performed. We compared the transcriptional profile of animals conditioned to migrate to the new temperature 17°C with that of animals conditioned to migrate to the previous temperature 23°C

2011-06-23 | GSE28856 | GEO

One-day thermal regime extends lifespan

Project description:Environmental factors such as temperature can modulate animal’s lifespan. However, the underlying mechanisms remain largely undefined. Through proteomic analysis of C. elegans at different time points (young adult, middle age, and old age) and under two temperature conditions (20°C and 25°C), we found that temperature affects C. elegans lifespan largely by modulating the proteostasis. Surprisingly, although animals live shorter at the higher temperature, we found that worms cultured at 25°C for one day at early adulthood promotes the protein homeostasis by decreasing the synthesis and increasing the degradation, suggesting the beneficial effects. Consistent with the finding, animals shifting from 20°C to 25°C for 24 hours between the larval L4 to adult Day 3 stages indeed live longer and are more resistant to stresses. Furthermore, we found that the one-day thermal induced lifespan extension is mediated by the FOXO transcriptional factor DAF-16. These results reveal an unexpected and complicated mechanism underlying the temperature effects on aging, which could potentially aid to develop strategies for treating aging related diseases.

2023-03-11 | PXD024916 | Pride

Expression analysis of Caenorhabditis elegans Bristol N2 rsd-2 and rsd-6 single mutants at 25Â°C and 20Â°C

Project description:Investigation of whole genome gene expression level changes in early generation Caenorhabditis elegans Bristol N2 rsd-2 and Bristol N2 rsd-6 single mutants, compared to late-generation strains at 25Â°C and 20Â°C A six chip study using total RNA recovered from two separate alleles of Caenorhabditis elegans Bristol N2 rsd-2 and one allele Bristol N2 rsd-6 , in which the effects of transgeneration aging are studied in early generation animals and late generation animals at the restrictive temperature of 25Â°C and the permissive temperature, 20Â°C.

2013-06-01 | E-GEOD-40459 | biostudies-arrayexpress

Proteomics analysis of Hypsizygus marmoreus

Project description:Hypsizygus marmoreus is one of the most popular industrialized cultivation mushrooms in East Asia. H. marmoreus is the third wildly cultivated industrialized cultivated mushroom in China now behind only Flammulina velutipes and Pleurotus eryngii. H. marmoreus is a low-temperature fruiting mushroom. The mycelia grow vegetatively at 23 °C to 25 °C and transform into fruiting process at 13 °C to 17 °C. The fruiting process of H. marmoreus is sensitive to temperature, and high temperature can lead to the death of mycelia and malformation of the fruiting body. Therefore, thermotolerance is important for H. marmoreus during both vegetative growth and fruiting-body formation. Previous studies on H. marmoreus have mainly focused on cultivation, nutrition and bioactive compounds extracted, but little is known about thermotolerance. The aim of this project is to elucidate the thermotolerance mechanism of Hypsizygus marmoreus.

2020-12-14 | PXD017654 | Pride

Microarray analysis of TAP::ALG-1 associated RNAs isolated from synchronized 'wild-type' animals and 'mir-58' mutants

Project description:To discover new miRNA targets, we generated a C. elegans transgenic line expressing a functional N-terminally Tandem Affinity Purification (TAP) tagged ALG-1 protein (C. elegans strain WS4303). We crossed the TAP::ALG-1 transgene into the mir-58(n4640) mutant background to generate the strain WS5041. For simplicity, we will hereafter term the TAP::ALG-1 transgenic animals as wild typeand the transgenic WS5041 animals as mir-58. We compared the mRNA population that coimmunopurified with TAP::ALG-1 from synchronized L4 stage wild-type animals with that from synchronized L4 stage mir-58 mutant animals by one-color Affymetrix gene arrays. miR-58 target mRNAs should be specifically underrepresented in the latter samples. Strains WS4303 (wt) and WS5041 (mir-58) were used for TAP::ALG-1 IPs. All experiments were conducted in three independent replicates. For each replicate, WS4303 and WS5041 were grown in parallel. 150 ng of TAP::ALG-1 associated RNA isolated from synchronized late L4 animals were sent to the GeneCore facilty in Heidelberg, Germany (http://www.genecore.embl.de/index.cfm), and the microarray data were generated according to their standard protocol (Weinmann et al. 2009).

2012-03-01 | E-GEOD-32942 | biostudies-arrayexpress

Quantitative temporal phosphoproteomics of aging C.elegans under different environmental temperatures

Project description:Temperature is one of the primary environmental factors that affect aging, in which protein phosphorylation is an important regulator. Currently, the understanding of phosphorylation events in regulatory networks during aging has remained rather limited. Therefore, the phosphoproteomes of C.elegans of different age groups cultured at 20°C in natural aging process and 25°C in accelerated aging process were analyzed. Through using the iTRAQ-labeled phosphoproteomics method, 2375 phosphoproteins and 9063 phosphosites were identified. Volcano plots illustrated that 208 proteins during natural aging and 130 during accelerated aging, were significantly changed. Gene ontology and pathway analysis revealed that these proteins were mainly involved in temperature response, DNA transcription, protein translation, tissue system development and animal behavior processes. Moreover, our results uncovered those kinases CK2, MAPK and CAMK2 might play important roles in aging regulation. In summary, our results provided a new insight into the complicated phosphor-regulatory network system during aging and an important resource for future studies of protein phosphorylation in worms.

2018-08-08 | PXD009661 | Pride

Identification of Transcription Factor SKN-1::GFP Binding Regions in L1

Project description:modENCODE_submission_2622 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP178(made_by : S Kim tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc119(ed3);wgIs178(skn-1::TY1 EGFP FLAG;unc119) official name : WBGene00004804 ); Developmental Stage: fed L1; Genotype: unc119(ed3);wgIs178(skn-1::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene skn-1; Strain OP178(made_by : S Kim tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc119(ed3);wgIs178(skn-1::TY1 EGFP FLAG;unc119) official name : WBGene00004804 ); temp (temperature) 20 degree celsius Series_type: CHIP-seq

2011-02-18 | E-GEOD-25810 | biostudies-arrayexpress

Identification of miRNA target genes in C. elegans by RIP-chip-SRM

Project description:RIP-chip-SRM : a New Combinatorial Large Scale Approach Identifies a Set of Translationally Regulated bantam/miR 58 Targets in C. elegans RNA binding protein immunopurification + microarray + targeted protein quantification via Selected Reaction Monitoring This SuperSeries is composed of the following subset Series: GSE32941: Purification of TAP::ALG-1 complexes and associated RNA from mixed-stage TAP::ALG-1 transgenic (WS4303) and wild-type (N2) animals GSE32942: Microarray analysis of TAP::ALG-1 associated RNAs isolated from synchronized 'wild-type' animals and 'mir-58' mutants GSE32943: Expression analysis of WS4303 (wild type) vs WS5041 (mir-58 mutants) total mRNA Refer to individual Series

2012-03-01 | E-GEOD-32944 | biostudies-arrayexpress

Identification of Transcription Factor EFL-1::GFP Binding Regions in Ab

Project description:modENCODE_submission_3605 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: DevStageWorm:L1 26dC:MS:1(official name : L1 26dC ); Developmental Stage: L1 larva; Genotype: wild type; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage L1 larva; Target gene efl-1; Strain DevStageWorm:L1 26dC:MS:1(official name : L1 26dC ); temp (temperature) 20 degree celsius

2013-07-11 | E-GEOD-48703 | biostudies-arrayexpress

Identification of Transcription Factor LSY-2::GFP Binding Regions in Starved

Project description:modENCODE_submission_3846 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: DevStageWorm:starved L1:MS:1(official name : starved L1 ); Developmental Stage: L1 larva; Genotype: unc-119(ed3); wgIs367(lsy-2::TY1 EGFP FLAG; unc-119); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage L1 larva; Target gene lsy-2; Strain DevStageWorm:starved L1:MS:1(official name : starved L1 ); temp (temperature) 20 degree celsius

2013-07-11 | E-GEOD-48717 | biostudies-arrayexpress

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