Transcriptional profile of C. elegans following RNAi of elt-2 [L1 stage]
Ontology highlight
ABSTRACT:
ORGANISM(S): Caenorhabditis elegans
SUBMITTER: Stuart Kim
PROVIDER: E-GEOD-69261 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:We used RNA-seq to identify 292 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-69262 | 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: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: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:In this study we show that global levels of mature miRNAs are unaffected in C. elegans after knockdown of either subunit of CK2 (encoded by kin-3 and kin-10) by RNAi. Small RNAs were quantified from wild-type animals at L4 stage fed either vector (L4440), kin-3, kin-10, or alg-1 RNAi. Mature miRNA counts were quantified by summing the total number of reads mapping to each miRNA and normalized to the total number of mapped reads per sequencing library.
2015-12-10 | E-GEOD-66764 | biostudies-arrayexpress
Project description:Transciptomic analysis of germline tumor cells to understand the role of autophagy and neuronal differentiation in lifespan extension. Methods: Worms were grown on control L444 seeded plates or gld-1 RNAi seeded plates and subjected to RNA isolation and sequencing using standard Illumina protocols. Conclusions: Fasting of animals expressing tumors increases their lifespan two-fold through autophagy and modular changes in transcription as well as metabolism.
2016-01-15 | E-GEOD-65406 | biostudies-arrayexpress
Project description:This project includes 20 samples after immunoprecipitation of C. elegans myosin heavy chain B (MHC B/UNC-54/F11C3.3, UniProt P02566 with a Gly387Arg mutation) in 4 replicates of 4 conditions. Lysates from a myosin-misfolding C. elegans strain (unc-54(e1301) with a Gly387Arg substitution in MHC B) grown on (A) control RNAi, (B) RNAi against nhl-1 (F54G8.4), (C) RNAi against F40A3.6, and (D) RNAi against nhl-1 and F40A3.6 together were used for immunoprecipitation. Samples from groups A, B, C and D were incubated over night at 4°C with 1 µg of a mouse monoclonal hybridoma antibody against MHC B (mAb 5-8 from the Developmental Studies Hybridoma Bank, DSHB), while 4 lysate samples from unc-54(e1301) worms on control RNAi (Z) were incubated WITHOUT antibody addition. The next day, co-immunoprecipitated proteins were collected on magnetic Dynabeads Protein A for 2 h at 4°C, washed, on-bead digested, and subjected to identification by mass spectrometry.
2024-07-16 | PXD045076 | Pride