Transcriptional profile of C. elegans following RNAi of elt-2 [L4 stage]
Ontology highlight
ABSTRACT:
ORGANISM(S): Caenorhabditis elegans
SUBMITTER: Stuart Kim
PROVIDER: E-GEOD-69262 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:We used RNA-seq to identify 162 genes that are differentially-regulated following elt-2 RNAi Whole-worm mRNA was sequenced from elt-2 RNAi- and control-fed worms. Biological triplicates were assay for each condition
2016-03-22 | E-GEOD-69261 | biostudies-arrayexpress
Project description:We used RNA-seq to discover that gene expression changes during aging are attenuated in elt-2 overexpressors relative to controls Whole-worm mRNA was sequenced from worms over-expressing elt-2 and control worms. Five biological replicates were collected for each condition.
2016-03-22 | E-GEOD-69263 | biostudies-arrayexpress
Project description:We performed RNA-seq to quantify gene expression changes in adult worms upon knockdown of transcription factor unc-62/Homothorax. unc-62 is a developmental regulator that binds proximal to age-regulated transcripts and modulates lifespan. In the intestine (in which tissue-specific unc-62 knockdown increases lifespan), we identify multiple effects of unc-62 knockdown linked to extension of longevity. First, unc-62 RNAi decreases the expression of yolk proteins (vitellogenins) that aggregate in the body cavity and become toxic in old age. Second, unc-62 RNAi results in a broad increase in expression of intestinal genes that typically decrease expression with age, suggesting that unc-62 activity balances intestinal resource allocation between yolk protein expression and fertility on the one hand and somatic functions on the other. mRNA profiling by Illumina HiSeq of 3 biological replicates of day 4 adult Caenorhabditis elegans that were fed either control or unc-62 RNAi beginning at day 1 of adulthood.
2012-09-01 | E-GEOD-39574 | biostudies-arrayexpress
Project description:modENCODE_submission_4789 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: OP75(official name : OP75 genotype : unc-119 (ed3) III; wgIs75 [elt-3::TY1::EGFP::FLAG; unc-119 (+)] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The ELT-3::EGFP fusion protein is expressed in the correct elt-3 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ELT-3 transcription factor. made_by : R Waterston ); Developmental Stage: embryo; Genotype: unc-119 (ed3) III; wgIs75 [elt-3::TY1::EGFP::FLAG; unc-119 (+)]; Sex: mixed Male and Hermaphrodite population; EXPERIMENTAL FACTORS: Developmental Stage embryo; Target gene elt-3; Strain OP75(official name : OP75 genotype : unc-119 (ed3) III; wgIs75 [elt-3::TY1::EGFP::FLAG; unc-119 (+)] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The ELT-3::EGFP fusion protein is expressed in the correct elt-3 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ELT-3 transcription factor. made_by : R Waterston ); temp (temperature) 20 degree celsius
2013-05-11 | E-GEOD-46777 | biostudies-arrayexpress
Project description:modENCODE_submission_4632 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: OP354(official name : OP354 genotype : unc119(ed3);wgIs354(elt-1::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. made_by : Bob Waterston's lab from UW ); Developmental Stage: L2; Genotype: unc119(ed3);wgIs354(elt-1::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage L2; Target gene elt-1; Strain OP354(official name : OP354 genotype : unc119(ed3);wgIs354(elt-1::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. made_by : Bob Waterston's lab from UW ); temp (temperature) 20 degree celsius
2013-05-11 | E-GEOD-46773 | biostudies-arrayexpress
Project description:This project aims to investigate the metabolic pathways expressed by the active microbial community occurring at the deep continental subsurface. Subsurface chemoLithoautotrophic Microbial Ecosystems (SLiMEs) under oligotrophic conditions are supported by H2; however, the overall ecological trophic structures of these communities are poorly understood. Some deep, fluid-filled fractures in the Witwatersrand Basin, South Africa appear to support inverted trophic pyramids wherein methanogens contributing <5% of the total DNA apparently produce CH4 that supports the rest of the community. Here we show the active metabolic relationships of one such trophic structure by combining metatranscriptomic assemblies, metaproteomic and stable isotopic data, and thermodynamic modeling. Four autotrophic β-proteobacteria genera that are capable of oxidizing sulfur by denitrification dominate. They co-occur with sulfate reducers, anaerobic methane oxidizers and methanogens, which each comprises <5% of the total community. Defining trophic levels of microbial chemolithoautotrophs by the number of transfers from the initial abiotic H2-driven CO2 fixation, we propose a top-down cascade influence of the metabolic consumers that enhances the fitness of the metabolic producers to explain the inverted biomass pyramid of a multitrophic SLiME. Symbiotic partnerships are pivotal in the deep biosphere on and potentially beyond the Earth.
2018-10-27 | PXD004634 | Pride
Project description:We used RNA-seq to assay gene expression changes over time in response to OP50 and PY79 To understand the molecular processes underlying aging, we screened modENCODE ChIP-seq data to identify transcription factors that bind to age-regulated genes in C. elegans. The most significant hit was the GATA transcription factor encoded by elt-2, which is responsible for inducing expression of intestinal genes during embryogenesis. Expression of ELT-2 decreases during aging, beginning in middle age. We identified genes regulated by ELT-2 in the intestine during embryogenesis, and then showed that these developmental genes markedly decrease in expression as worms grow old. Overexpression of elt-2 extends lifespan and slows the rate of gene expression changes that occur during normal aging. Thus, our results identify the developmental regulator ELT-2 as a major driver of normal aging in C. elegans. Whole-worm mRNA was sequenced from E. coli- and B.subtilis-fed worms. For each condidtion, one replicate was sequenced at Day 4 and Day 13
2016-03-22 | E-GEOD-79415 | biostudies-arrayexpress
Project description:The complexity of metazoan organisms requires precise spatiotemporal regulation of gene expression during development. To identify different modes of developmental gene regulation we measured the transcriptome throughout development of the nematode Caenorhabditis elegans by mRNA sequencing with high temporal resolution. We find that approximately 2,000 transcripts undergo expression oscillations synchronized with larval transitions while thousands of genes are expressed in temporal gradients, similar to known timing regulators. By counting transcripts in individual animals, we show that the pulsatile expression of the microRNA (miRNA) lin-4 maintains the temporal gradient of its target lin-14 by dampening its expression oscillations. Our results demonstrate that this insulation is optimal when pulsatile expression of the miRNA and its target is synchronous. We propose that such a miRNA-mediated incoherent feed-forward loop is a potent filter that prevents propagation of potentially deleterious gene expression fluctuations during the development of an organism. We analyzed RNA-seq data of wild-type worms at two different temperatures, 20C and 25C, from samples picked every 2hrs and 1.5 hrs, resspectively, spanning all larval stages (L1,L2,L3,L4). At 20C we picked samples for L1-L3 (sample DH2: 0 hrs to 38 hrs) and for L4 (sample DH5: 38 hrs to 48 hrs) from independent populations. At 25C, all samples were picked from the same worm population (sample DH3: 0 hrs to 28.5 hrs). This time course ends at 28.5 hrs since at higher temperature nematode development is accelarated. Finally, we measured mRNA expression at 20C in a lin-4 knockout mutant worm (lin-4(e912)), again spanning all larval stages (sample DH4: 0 hrs to 48 hrs). Each sequencing sample consisted of a mixture of all time points with mRNA from different time points barcoded with Illumina barcodes and was sequenced on one or more lanes (DH2: 3 lanes; DH3: 3 lanes; DH4: 4 lanes; DH5: 1 lane) of an Illumina HiSeq2000.
2013-09-15 | E-GEOD-49043 | biostudies-arrayexpress
Project description:The centromere is a defining feature of eukaryotic chromosomes and is essential for the segregation of chromosomes during cell division. Centromeres are universally marked by the histone variant cenH3 and are restricted to specialized chromatin that most commonly localized to a single position along the chromosome. However, the DNA on which centromeric nucleosomes assemble is not conserved and varies greatly in size and composition. It ranges from genetically defined point centromeres that assemble a single cenH3-containing nucleosome to epigenetically defined regional centromeres embedded in megabases of tandemly repeated DNA to holocentromeres that extend along the length of the entire chromosomes. The organization of regional and holocentric centromeres has so far been elusive, as the precise locations of cenH3-containing sequences could not be determined. Our results show that the point centromere is the basic unit of holocentromeres and provide a basis for understanding how centromeric chromatin is maintained. We use high-resolution mapping of cenH3-associated DNA to show that Caenorhabditids elegans holocentromeres are organized as dispersed but discretely localized point centromeres.
2014-04-08 | E-GEOD-44412 | biostudies-arrayexpress
Project description:Parasitism is a major ecological niche for a variety of nematodes. Multiple nematode lineages have specialized as pathogens, including deadly parasites of insects that are used in biological control. We have sequenced and analyzed the draft genomes and transcriptomes of the entomopathogenic nematode Steinernema carpocapsae and four congeners (S. scapterisci, S. monticolum, S. feltiae, S. glaseri) distantly related to Caenorhabditis elegans. We used these genomes to establish phylogenetic relationships, explore gene conservation across species, identify genes uniquely expanded in insect parasites, and to identify conserved non-coding regulatory motifs that influence similar biological processes. Protein domain analysis of these genomes reveals a striking expansion of numerous putative parasitism genes including certain protease and protease inhibitor families as well as fatty acid- and retinol-binding proteins. We identify rapid evolution and expansion of the important developmental Hox gene cluster and identify novel conserved non-coding regulatory motifs associated with orthologous genes in Steinernema and Caenorhabditis. The deep conservation of the network of non-coding DNA motifs between these two genera for a subset of orthologous genes involved in neurogenesis and embryonic development suggests that a kernel of protein-DNA relationships is conserved through nematode evolution. We analyzed the gene expression of a total of 24 RNA-seq samples from 3 nematode species( S. carpocapsae, S. feltiae, and C. elegans) for comparative analysis. We collected the RNA at four developmental time points (mixed embryo, L1, infective juvenile/dauer, young adult) for each species in replicates.
2015-06-05 | E-GEOD-68588 | biostudies-arrayexpress