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Caenorhabditis japonica

ABSTRACT: Caenorhabditis japonica

PROVIDER: PRJNA12591 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	ABLE03.dat.gz	Other
	ABLE03.fasta.gz	Fasta.gz
	ABLE03.master.dat	Other
	SRR068436.fastq.gz	Fastqsanger.gz
	SRR068437.fastq.gz	Fastqsanger.gz

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Caenorhabditis japonica

Project description:Caenorhabditis japonica high resolution developmental transcriptomic time-course

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Caenorhabditis sex-specific RNAseq

Project description:This project defines the transcriptomes of XO (male) and XX (female or mutant pseudo-female) Caenorhabditis nematodes. The data allow the overall composition and sexual regulation of the transcriptome within a single species to be determined. In addition, the five related species studied allow meta-comparisons between them. Because two of the five (C. elegans and C. briggsae) produce a self-fertile XX hermaphrodite, while the XX sex in the remaining three (C. japonica, C. remanei, and C. brenneri) are true females, the data are particularly useful for inferring effects of sexual mode on genome-wide gene expression. L4 larvae and adults were pooled for each sex for five species (C. elegans, C. briggsae, C. japonica, C. brenneri, and C. remanei). Each of these 10 species-sex combinations was replicated three times, for a total of 30 samples.

2012-10-25 | E-GEOD-41367 | biostudies-arrayexpress

Caenorhabditis sex-specific RNAseq

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Caenorhabditis japonica high resolution developmental transcriptomic time-course

Project description:Transcriptomic studies typically examine expression at the gene level, although it has been long recognized that the same genetic locus may produce isoforms distinct in their splicing and site of polyadenylation. Here we examine alternatively polyadenylated (APA) transcripts throughout embryogenesis and discover distinct strategies for gene regulation. We introduce APA-Seq, an RNA-Seq method to study APA at a global level, and apply it to study individual C. elegans embryos throughout early development. Surprisingly, we find that genes, whose overall expression is constitutive throughout development, generally show highly dynamic expression for individual isoforms. Such genes tend to participate in cellular as opposed to developmental processes, and this trend was also evident in the closely related C. japonica nematode, providing evidence that the manner by which cellular processes are regulated during embryogenesis is evolutionarily conserved. Finally, we report that genes with dynamic isoform usage have significantly more miRNA binding sites relative to constitutively-expressed isoforms, suggesting strong miRNA regulation in the control of isoform expression. Our findings support a model distinguishing two modes of gene regulatory underlying embryonic development each with unique functions and mechanisms.

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Project description:To determine the distribution of centromere units in the genome of holocentric Chionographis japonica, we performed CENH3-ChIPseq using the customized species-specific CENH3 antibody. We mixed the chromatins of C. japonica and Secale cereal (inbred line Lo7) to dilute the highly abundant centromeric Chio satellite repeats (16%) in the C. japonica genome before immunoprecipitation. In addition, to determine the large-scale genome organization, we performed ChIPseq by targeting the evolutionarily conserved eu- and heterochromatin-specific histone marks H3K4me2 and H33K9me2

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Project description:We used proteomic analysis to reveal molecular response of Saccharina japonica to the projected ocean acidification conditions.

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