Caenorhabditis elegans
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ABSTRACT:
PROVIDER: PRJNA116677 | ENA |
REPOSITORIES: ENA
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Project description:Expression data from C. elegans during L4, L4-lethargus, and Adult
| PRJNA198532 | ENA
Project description:We applied a middle-down proteomics strategy for large scale protein analysis during in vivo development of Caenorhabditis elegans. We characterized post-translational modifications (PTMs) on histone H3 N-terminal tails at eight time points during the C. elegans lifecycle, including embryo, larval stages (L1 to L4), dauer and L1/L4 post dauer. Histones were analyzed by our optimized middle-down protein sequencing platform using high mass accuracy tandem mass spectrometry. This allows quantification of intact histone tails and detailed characterization of distinct histone tails carrying co-occurring PTMs. We measured temporally distinct combinatorial PTM profiles during C. elegans development. We show that the doubly modified form H3K23me3K27me3, which is rare or non-existent in mammals, is the most abundant PTM in all stages of C. elegans lifecycle. The abundance of H3K23me3 increased during development and it was mutually exclusive of the active marks H3K18ac, R26me1 and R40me1, suggesting a role for H3K23me3 in to silent chromatin. We observed distinct PTM profiles for normal L1 larvae and for L1-post dauer larvae, or L4 and L4 post-dauer, suggesting that histone PTMs mediate an epigenetic memory that is transmitted during dauer formation. Collectively, our data describe the dynamics of histone H3 combinatorial code during C. elegans lifecycle and demonstrate the feasibility of using middle-down proteomics to study in vivo development of multicellular organisms.
2015-11-02 | PXD002525 | Pride
Project description:Most organisms have an endogenous circadian clock that is synchronized to environmental signals such as light and temperature. Although circadian rhythms have been described in the nematode C. elegans at the behavioral level, these rhythms appear to be relatively non-robust. Moreover, in contrast to other animal models, no circadian transcriptional rhythms have been identified. Thus, whether this simple nematode contains a bona fide circadian clock remains an open question. We used microarray experiments to identify light- and temperature-regulated transcriptional rhythms in C. elegans, and show that subsets of these transcripts are regulated in a circadian manner. In addition, we find that light and temperature also globally drive the expression of many genes, indicating that C. elegans exhibits systemic responses to these stimuli. Populations of growth-synchronized wild-type C. elegans L1 larvae were entrained for 5 days until adulthood to 12:12 hr light/dark (LD) cycles (500-1000 lux) at a constant temperature of 18°C, or for 4 days to 12:12 hr temperature cycles (25:15°C - warm/cold or WC) in constant darkness. RNA was collected every 4 hrs during the last entrainment and the subsequent free-running days and analyzed via hybridization of Affymetrix GeneChips. L4 larvae were transferred to FUDR-containing plates to inhibit embryonic development.
2010-08-31 | E-GEOD-23528 | biostudies-arrayexpress
Project description:small RNA gene expression profiles of C. elegans in 4 age groups. The RNA-seq data comprise 4 age groups (1, 5, 10 and 20 days after L4). Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)
2021-10-19 | GSE110847 | GEO
Project description:Aging has been shown to be under genetic control in C. elegans. We performed Affymetrix micorarray-based transcriptional profililng of wild type C. elegans strain Bristol N2 during aging to detect temporal changes in gene expression. RNA was prepared for hybridization to Affy microarrays from synchronized populations of C. elegans at three points during aging: 1) the late larval L4 stage, 2) day 6 of adulthood, and 3) day 15 of adulthood.
2011-05-11 | E-GEOD-21784 | biostudies-arrayexpress
Project description:In this study, we exposed Caenorhabditis elegans wild types N2 to water collected from six sources in the Dutch village Sneek. The sources were: wastewater from a hospital, a community (80 households), a nursing home, influent into the local municipal wastewater treatment plant, effluent of the wastewater treatment plant, and surface water samples. The goal of the experiment was to determine if C. elegans can be used to identify pollutants in the water by transcriptional profiling. Age synchronized worms at developmental L4 larval stage were exposed to treatment for 24 hours. After flash freezing the samples, RNA was isolated, labeled and hybridized on oligo microarray (Agilent) slides.
2022-12-03 | E-MTAB-11260 | biostudies-arrayexpress
Project description:Comparison of gene expression profiles from C. elegans mutant strains (MIR73, MIR75 or MIR77) overexpressing genes involved in proline metabolism (B0513.5 or T22H6.2) with wildtype strain (N2) at 5 days after L4 larvae stage. Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)
2021-10-19 | GSE110842 | GEO
Project description:Comparison of gene expression profiles from C. elegans mutant strain CF1038 treated with L4440 and K02A4.1 RNAi and C. elegans mutant strain TU3311 treated with L4440 and B0412.2 RNAi for 5 days after L4 larvae stage. Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)
2021-10-19 | GSE110840 | GEO
Project description:In nature, animals often face feast or famine conditions. We aimed to identify the miRNAs of Caenorhabditis elegans that changed their expression under starvation conditions in stage L4 larvae. Our results highlight 14 miRNAs that show differential expression in starved versus well-fed larvae. In particular, miRNAs of the miR-35-3p/miR-41-3p family were upregulated 6-20 fold upon starvation. We verified the upregulation of miR-35-3p with qPCR. Additionally, we showed that the expression of gld-1, important in ovogenesis, and a validated target of miR-35-3p, was downregulated when the expression of miR-35-3p was higher. This study represents a starting point for a more comprehensive understanding of the role of miRNAs during starvation in C. elegans. Illumina small RNA sequencing of starved and well-fed L4 worms.
2016-01-27 | E-GEOD-67711 | biostudies-arrayexpress