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Caenorhabditis elegans isolate:Hawaiian and Bristol

ABSTRACT: Caenorhabditis elegans isolate:Hawaiian and Bristol Genome sequencing

PROVIDER: PRJNA699586 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13740600_1.fastq.gz	Fastqsanger.gz
	SRR13740600_2.fastq.gz	Fastqsanger.gz
	SRR13740601_1.fastq.gz	Fastqsanger.gz
	SRR13740601_2.fastq.gz	Fastqsanger.gz
	SRR13740602_1.fastq.gz	Fastqsanger.gz

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Caenorhabditis elegans strain:Hawaiian isolate (CB4856)

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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 25Â°C and 20Â°C A six chip study using total RNA recovered from two separate alleles of Caenorhabditis elegans Bristol N2 rsd-2 and one allele Bristol N2 rsd-6 , in which the effects of transgeneration aging are studied in early generation animals and late generation animals at the restrictive temperature of 25Â°C and the permissive temperature, 20Â°C.

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Expression data from ageing wt N2 Bristol Caenorhabditis elegans population.

Project description:Expression data from ageing wt N2 Bristol Caenorhabditis elegans population.

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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. Twelve C. elegans natural isolate samples were studied. There were no replicates or dye-swap hybridizations.

2010-05-17 | E-GEOD-19440 | biostudies-arrayexpress

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