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Caenorhabditis elegans

ABSTRACT: Whole genome sequencing of the N2 strain of C. elegans.

PROVIDER: PRJDB2670 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR008443_1.fastq.gz	Fastqsanger.gz
	DRR008443_2.fastq.gz	Fastqsanger.gz
	DRR008444_1.fastq.gz	Fastqsanger.gz
	DRR008444_2.fastq.gz	Fastqsanger.gz
	DRR008445_1.fastq.gz	Fastqsanger.gz

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Caenorhabditis elegans strain:N2

Project description:Caenorhabditis elegans strain:N2 Genome sequencing

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Caenorhabditis elegans strain:N2

Project description:Caenorhabditis elegans strain:N2 Genome sequencing

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Caenorhabditis elegans strain:N2

Project description:Caenorhabditis elegans strain:N2 Genome sequencing

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Expression analysis of Caenorhabditis elegans Bristol N2 prg-1 and Bristol N2 prg-1; daf-2 double mutant

Project description:Investigation of whole genome gene expression level changes in early generation Caenorhabditis elegans Bristol N2 prg-1 and Bristol N2 prg-1; daf-2 double mutant, compared to late-generation strains.

2013-06-01 | GSE40569 | GEO

Sequencing of Caenorhabditis elegans overexpression mutants.

Project description:Comparison of gene expression profiles from C. elegans mutant strains (MIR73, MIR75 or MIR77) overexpressing genes involved in proline metabolism (B0513.5 or T22H6.2) with wildtype strain (N2) at 5 days after L4 larvae stage. Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

2021-10-19 | GSE110842 | GEO

Copy number variation in the genomes of twelve natural isolates of Caenorhabditis elegans

Project description:Background: Copy number variation is an important component of genetic variation in higher eukaryotes. The extent of natural copy number variation in C. elegans is unknown outside of 2 highly divergent wild isolates and the canonical N2 Bristol strain. Results: We have used array comparative genomic hybridization (aCGH) to detect copy number variation in the genomes of 12 natural isolates of Caenorhabditis elegans. Deletions relative to the canonical N2 strain are more common in these isolates than duplications, and indels are enriched in multigene families on the autosome arms. Among the strains in our study, the Hawaiian and Madeiran strains (CB4856 and JU258) carry the largest number of deletions, followed by the Vancouver strain (KR314). Overall we detected 510 different deletions affecting 1136 genes, or over 5% of the genes in the canonical N2 genome. The indels we identified had a median length of 2.7 kb. Since many deletions are found in multiple isolates, deletion loci were used as markers to derive an unrooted tree to estimate genetic relatedness among the strains. Conclusion: Copy number variation is extensive in C. elegans, affecting over 5% of the genes in the genome. The deletions we have detected in natural isolates of C. elegans contribute significantly to the number of deletion alleles available to researchers. The relationships between strains are complex and different regions of the genome possess different genealogies due to recombination throughout the natural history of the species, which may not be apparent in studies utilizing smaller numbers of genetic markers.

2009-12-17 | GSE19440 | GEO

Expression analysis of Caenorhabditis elegans Bristol N2 rsd-2 and rsd-6 single mutants at 25°C and 20°C

Project description:Investigation of whole genome gene expression level changes in early generation Caenorhabditis elegans Bristol N2 rsd-2 and Bristol N2 rsd-6 single mutants, compared to late-generation strains at 25°C and 20°C

2013-06-01 | GSE40459 | GEO

Caenorhabditis elegans infected with Enterococcus

Project description:Young adult N2 Caenorhabditis elegans were infected with Enterococcus faecalis or Enterococcus faecium for 8 h to determine the transcriptional host response to each enterococcal species. Analysis of differential gene expression in C. elegans young adults exposed to four different bacteria: heat-killed Escherichia coli strain OP50 (control), wild-type E. faecalis MMH594, wild-type E. faecium E007, or Bacillus subtilis PY79 (sigF::kan). Samples were analyzed at 8 hours after exposure to the different bacteria. These studies identified C. elegans genes induced by pathogen infection. Brain-heart infusion agar plates (10 ug/ml kanamycin) were used.

2018-02-14 | GSE95636 | GEO

Identification of GFP-SPT-2 binding sites in the Caenorhabditis elegans genome

Project description:We aimed at investigating whether the newly identified C. elegans SPT2 histone chaperone controls chromatin structure. We decided to profile SPT-2 binding sites to identify its genomic targets and we performed GFP ChIP-seq on a C. elegans strain expressing endogenously GFP-tagged SPT-2, using WT N2 untagged worms as control for binding specificity.

2023-02-09 | GSE224800 | GEO

Transcriptome of microbiome for the nematode Caenorhabditis elegans

Project description:Host-microbe associations underlie many key processes of host development, immunity, and life history. Yet, none of the current research on the central model species Caenorhabditis elegans considers the worm’s natural microbiome. Instead, almost all laboratories exclusively use the canonical strain N2 and derived mutants, maintained through routine bleach sterilization in monoxenic cultures with an E. coli strain as food. Here, we characterize for the first time the native microbiome of C. elegans and assess its influence on nematode life history characteristics via transcriptomics.

2019-02-25 | GSE111364 | GEO

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