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Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling by array of C. elegans isolates treated with dauer larva-inducing pheromone

ABSTRACT: Microarray analyses were used to compare changes in gene expression between two sets of environmental conditions ('normal' and 'dauer larva-inducing') and between isolates (N2, DR1350, RIL-14, RIL-17). These comparisons were made in two experimental blocks: block one N2 and DR1350; block two RIL-14 and RIL-17. For each isolate there were three biological replicates for both set environmental conditions.

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Simon Harvey

PROVIDER: E-MEXP-1810 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Natural variation in gene expression in the early development of dauer larvae of Caenorhabditis elegans.

Harvey Simon C SC Barker Gary L A GL Shorto Alison A Viney Mark E ME

BMC genomics 20090718

<h4>Background</h4>The free-living nematode Caenorhabditis elegans makes a developmental decision based on environmental conditions: larvae either arrest as dauer larva, or continue development into reproductive adults. There is natural variation among C. elegans lines in the sensitivity of this decision to environmental conditions; that is, there is variation in the phenotypic plasticity of dauer larva development. We hypothesised that these differences may be transcriptionally controlled in ea ...[more]

PMID: 19615088

Similar Datasets

Transcription profiling by array of C. elegans isolates treated with dauer larva-inducing pheromone

Project description:Microarray analyses were used to compare changes in gene expression between two sets of environmental conditions ('normal' and 'dauer larva-inducing') and between isolates (N2, DR1350, RIL-14, RIL-17). These comparisons were made in two experimental blocks: block one N2 and DR1350; block two RIL-14 and RIL-17. For each isolate there were three biological replicates for both set environmental conditions.

2008-10-01 | E-MEXP-1808 | biostudies-arrayexpress

Extensive oscillatory gene expression during C. elegans larval development [RNA-seq for polyA enriched mRNAs]

Project description:We report the presence of extensive, transcriptionally controlled oscillations in the C. elegans, developmental transcriptome. Furthermore, using ribosome profiling, we show that these oscillating transcripts are actively translated. Examination of three timecourses that were collected over C. elegans development and analyzed by RNA-seq of mRNA libraries

2014-03-01 | E-GEOD-52861 | biostudies-arrayexpress

Dynamic changes of histone H3 marks during Caenorhabditis elegans lifecycle revealed by middle-down proteomics

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

Transcription profiling of C. elegans 12 hours and 24 hours post exposure to fungal pathogen, Drechmeria coniospora

Project description:Transcriptome study of C.elegans animals 12 hours and 24 hours post exposure to fungal pathogen, Drechmeria coniospora.

2007-07-04 | E-MEXP-479 | biostudies-arrayexpress

C. elegans: Dauers and Dauer-Exit at 12 hour time-point vs. Mix-stage worms

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 (separate data-sets on a custom microarray platform designed by us and manufactured by Agilent) , to study evolution of developmental pathways regulating dauer development. Two-condition experiments. Experiment 1 = Dauers vs. Mix-stage worms. 4 biological replicates for each condition, including 2 dye-swaps. Experiment 2 = Dauer-Exit at 12 hour time-point s vs. Mix-stage worms. 4 biological replicates for each condition, including 2 dye-swaps. Total samples from both experiments 1 and 2 = 8.

2011-07-27 | E-GEOD-30977 | biostudies-arrayexpress

P. pacificus : Dauers and Dauer-Exit at 12 hour time-point vs. Mix-stage worms

Project description:Transcriptional profiling of P. pacificus 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 C. elegans (see NCBI GEO series GSE30977) , to study evolution of developmental pathways regulating dauer development. Two-condition experiments. Experiment 1 = Dauers vs. Mix-stage worms. 4 biological replicates for each condition, including 2 dye-swaps. Experiment 2 = Dauer-Exit at 12 hour time-point s vs. Mix-stage worms. 3 biological replicates for each condition, including 1 dye-swaps. Total samples from both experiments 1 and 2 = 7.

2011-09-02 | E-GEOD-31861 | biostudies-arrayexpress

Extensive oscillatory gene expression during C. elegans larval development

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-03-01 | E-GEOD-52910 | biostudies-arrayexpress

Pristionchus pacificus and Caenorhabditis elegans: Dauer and Dauer exit versus mix-stage comparisons

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

Transcription profiling of C. elegans exposed to several different bacterial pathogens

Project description:Transcritome study of C.elegans exposed to multiple, different bacterial pathogens. Experiments were performed in set-replicates of either 3 or 5.<br> There are 3 for samples: Aeromonas hydrophila, Enterococcus faecalis, Erwinia carotovora and Photorhabdus luminescens. <br> There are 5 for samples: Serratia marcesens and Escherichia coli (control).<br>

2008-02-06 | E-MEXP-766 | biostudies-arrayexpress

Encyclopedia of C. elegans 3' UTRs and their regulatory elements

Project description:The 3' untranslated region (3'UTR) constitutes a major site of post-transcriptional regulation of gene expression. Sequence elements in the 3'UTR interact with trans-acting regulators such as microRNAs that affect translation and stability. The overall aim is to use a 3'RACE cloning-sequencing stragety to identify the 3'UTRs of C. elegans transcripts and explore their heterogeneity in different developmental stages and tissues. Keywords: Transcriptome analysis For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Raw data files are available on our FTP site: ftp://ftp.ncbi.nlm.nih.gov/pub/geosup/Series/GSE17781 pilot study [GSM443959..GSM443964]: N2 wildtype worms staged at embryo, L1, L2, L3, L4, and adult full experiment [GSM446651..GSM446661]: N2 wildtype worms staged at embryo, L1, L2, L3, L4, dauer, and adult. Illumina Genome Analyzer sequencing of isolated clones [GSM469439] 454 sequencing of RACE clones [GSM469976]

2009-09-01 | E-GEOD-17781 | biostudies-arrayexpress

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