Caenorhabditis elegans isolate:JU1395
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ABSTRACT:
PROVIDER: PRJNA622250 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR11456709_1.fastq.gz | Fastqsanger.gz |
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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:Global analysis of dauer gene expression in Caenorhabditis elegans
| PRJNA92707 | ENA
Project description:Transcriptional profiling of C. elegans worms from (1) dauer stage, or (2) dauer-exit at 12 hours stage, compared to mix-stage worms as a common reference. The goal was to determine genes regulated during dauer development and recovery or exit from dauer stage. This data was then compared to data generated for corresponding developmental stages in the nematode Pristionchus pacificus (see NCBI GEO series GSE31861) , to study evolution of developmental pathways regulating dauer development.
2011-07-28 | GSE30977 | GEO
Project description:Many organisms in the nature can drive themselves into an ametabolic state known as anhydrobiosis upon extreme desiccation. The nematode C. elegans is one of them. However, the anhydrobiotic ability of the worm is limited to a special developmental stage known as the dauer. Besides, the dauer larvae must be first treated by a mild desiccation stress (preconditioning) so that they gain desiccation tolerance. In this study, we investigated the differential gene expression during preconditioning in the C. elegans dauer.
2013-08-23 | E-MEXP-3899 | biostudies-arrayexpress
Project description:Both plasticity and robustness are pervasive features of developmental programs. The dauer in Caenorhabditis elegans is an alternative to the third larval stage of the nematode and is an example of phenotypic plasticity. The dauer is an arrested, hypometabolic state that undergoes dramatic changes in gene expression compared to conspecifics that continue development, and can be induced by several adverse environments or genetic mutations that act as independent and parallel inputs into the larval developmental program. However, given the different genetic or environmental triggers that can induce dauer, gene expression in dauer larvae could be invariant or vary depending on the larvae’s route into dauer entry; this question has not been examined. Here we use RNA-sequencing to characterize gene expression in dauer larvae induced to arrest development in response to different stimuli. By assessing the variance in the expression levels of all genes and computing the Spearman's rank-order correlation of gene expression within several Gene Ontologies (GO) and gene networks, we find that the expression patterns of most genes, except for those that act in specific defense and metabolic pathways, are strongly correlated between the different dauer larvae, suggestive of transcriptional robustness. We speculate that the transcriptional robustness of core dauer pathways allows for the buffering of variation in the expression of genes involved in their response to the environment, allowing the different dauers to be better suited to survive in and exploit different niches.
2024-08-15 | GSE274872 | GEO
Project description:These are the 94 microarray experiments that are published in the paper: John Wang and Stuart K. Kim. Global analysis of dauer gene expression in Caenorhabditis elegans, Development 2003 130: 1621-1634. There are 94 individual microarray experiments divided into 3 broad experiments. The first experiment is a time course of dauer exit; each time course is labeled as "Dauer MTC#". The second experiment is a time course of L1 development after starvation arrest; each time couse is labeled "L1 MTC#". The final experiment is a comparison of pure dauers (0 hours) versus 12 hours after dauer exit and are labeled "Dauer Adjust". Every time course was repeated 4 times (#N)however for the dauer 4 and 7 hour time points there are only 3 replicates. For instance, all the time points labeled as "Dauer MTC#1" are from the same starting pool of dauer worms that were aliquoted into 10 fractions and analyzed at the time indicated. Every sample is compared to a common reference RNA that is used throughout all the hybridizations. In some cases there is a "-2" after the hour designation; this means the first hybridization failed for some technical reason and thus the second hybridization (same RNA) is reported. Groups of assays that are related as part of a time series. Keywords: time_series_design
2005-08-20 | GSE3169 | GEO
Project description:These are the 94 microarray experiments that are published in the paper: John Wang and Stuart K. Kim. Global analysis of dauer gene expression in Caenorhabditis elegans, Development 2003 130: 1621-1634. There are 94 individual microarray experiments divided into 3 broad experiments. The first experiment is a time course of dauer exit; each time course is labeled as "Dauer MTC#". The second experiment is a time course of L1 development after starvation arrest; each time couse is labeled "L1 MTC#". The final experiment is a comparison of pure dauers (0 hours) versus 12 hours after dauer exit and are labeled "Dauer Adjust". Every time course was repeated 4 times (#N)however for the dauer 4 and 7 hour time points there are only 3 replicates. For instance, all the time points labeled as "Dauer MTC#1" are from the same starting pool of dauer worms that were aliquoted into 10 fractions and analyzed at the time indicated. Every sample is compared to a common reference RNA that is used throughout all the hybridizations. In some cases there is a "-2" after the hour designation; this means the first hybridization failed for some technical reason and thus the second hybridization (same RNA) is reported.
2005-07-13 | E-SMDB-1964 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE30977: C. elegans: Dauers and Dauer-Exit at 12 hour time-point vs. Mix-stage worms GSE31861: P. pacificus : Dauers and Dauer-Exit at 12 hour time-point vs. Mix-stage worms Refer to individual Series
2012-03-22 | E-GEOD-36644 | biostudies-arrayexpress
Project description:C. elegans complete proteome using Gel LC-MS. We compare the proeome of dauer and L3 larval stages
2024-05-22 | PXD048087 | Pride