Caenorhabditis elegans
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA326270 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We have adapted the eXcision Repair-sequencing (XR-seq) method to generate single-nucleotide resolution dynamic repair maps of UV-induced cyclobutane pyrimidine dimers (CPD) photoproducts in the Caenorhabditis elegans (C. elegans) genome.
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Project description:Caenorhabditis elegans high resolution developmental transcriptomic time-course
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Project description:The potential environmental risk of single-walled carbon nanotubes (SWCNTs) is evaluated using Caenorhabditis elegans (C. elegans) as an ecotoxicological animal model. Highly soluble amide-modified SWCNTs (a-SWCNTs) are used in the present study so that the dose-response impact of SWCNTs could be studied. mechanisms. a-SWCNTs are efficiently taken up by worms during feeding and cause significant toxicity in worms, including retarded growth, shortened lifespan and defective embryogenesis. Genome-wide gene expression analysis is performed to investigate the toxic molecular
2012-10-11 | GSE41486 | GEO
Project description:Deciphering the C. elegans embryonic transcriptome with tissue, time, and alternative splicing resolution
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Project description:Recently developed single cell technologies allow researchers to characterize cell states at ever greater resolution and scale. C. elegans is a particularly tractable system for studying development, and recent single cell RNA-seq studies characterized the gene expression patterns for nearly every cell type in the embryo and at the second larval stage (L2). Gene expression patterns are useful for learning about gene function and give insight into the biochemical state of different cell types; however, in order to understand these cell types, we must also determine how these gene expression levels are regulated. We present the first single cell ATAC-seq study in C. elegans. We collected data in L2 larvae to match the available single cell RNA-seq data set, and identify tissue-specific chromatin accessibility patterns that align well with existing data, including the L2 single cell RNA-seq results. Using a novel implementation of the Latent Dirichlet Allocation algorithm, our chromatin accessibility data provide new insights into which genomic loci may be participating in cell type-specific gene regulation, with promise for better understanding of cellular differentiation and gene regulation in the worm.
2021-04-12 | GSE157017 | GEO
Project description:The potential environmental risk of single-walled carbon nanotubes (SWCNTs) is evaluated using Caenorhabditis elegans (C. elegans) as an ecotoxicological animal model. Highly soluble amide-modified SWCNTs (a-SWCNTs) are used in the present study so that the dose-response impact of SWCNTs could be studied. mechanisms. a-SWCNTs are efficiently taken up by worms during feeding and cause significant toxicity in worms, including retarded growth, shortened lifespan and defective embryogenesis. Genome-wide gene expression analysis is performed to investigate the toxic molecular We examined the effect of different concentrations of a-SWCNTs (0, 100, 250 and 500 μg/mL) on the growth of C. elegans. We measured the body length of worms reaching the L4 stage after a-SWCNT exposure for 48 hr at 22°C. Compared to the untreated worms, we found that the average length of worms exposed to a-SWCNTs (500 μg mL-1) was significantly shorter than the untreated groups. In addition, the dose of a-SWCNTs also caused retarded growth, reduced lifespan and defective embryogenesis in worms. Genome-wide gene expression analysis using an Affymetrix GeneChip was performed to further investigate the molecular basis of these defects.
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Project description:A high resolution transcriptome map for both wild-type and NMD defective C. elegans
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Project description:Alternative splicing (AS) plays a crucial role in the diversification of gene function and regulation. Consequently, the systematic identification and characterization of temporally regulated splice variants is of critical importance to understanding animal development. We have used high-throughput RNA sequencing and microarray profiling to analyze AS in C. elegans across various stages of development. This analysis identified thousands of novel splicing events, including hundreds of developmentally regulated AS events. To make these data easily accessible and informative, we constructed the C. elegans Splice Browser, a web resource in which researchers can mine AS events of interest and retrieve information about their relative levels and regulation across development. The data presented in this study, along with the Splice Browser, provides the most comprehensive set of annotated splice variants in C. elegans to date, and is therefore expected to faciliate focused, high resolution in vivo functional assays of AS function.
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Project description:Single-cell transcriptomes of each cell of the C. elegans embryo until the 16-cell stage
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Project description:A lineage-resolved molecular atlas of C. elegans embryogenesis at single cell resolution
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