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Strongylocentrotus purpuratus

ABSTRACT: Select microRNAs are essential for early development in the sea urchin.

PROVIDER: PRJNA151931 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR409091.fastq.gz	Fastqsanger.gz
	SRR409092.fastq.gz	Fastqsanger.gz
	SRR409093.fastq.gz	Fastqsanger.gz
	SRR409094.fastq.gz	Fastqsanger.gz
	SRR409095.fastq.gz	Fastqsanger.gz

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Base-resolution DNA methylation maps of purple sea urchin (Strongylocentrotus purpuratus)

Project description:Using MethylC-seq we investigated single-base resolution methylomes of sea urchin during development.

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Response to elevated pCO2 in Strongylocentrotus purpuratus larvae

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Base-resolution DNA hydroxymethylation maps of purple sea urchin (Strongylocentrotus purpuratus), european lancelet (Branchiostoma lanceolatum) and zebrafish (Danio rerio) using ACE-seq

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Response to elevated pCO2 in Strongylocentrotus purpuratus larvae

Project description:Transcriptional profiling of purple sea urchin (Strongylocentrotus purpuratus) larvae cultured under three different seawater CO2 concentrations 400, 800, 1200 M-BM-5atm. The goal was to determine the effects of CO2, an important climate change variable, on global gene expression Larvae were cultured under three different seawater CO2 concentrations 400, 800, 1200 M-BM-5atm, each with four replicate cultures, and sampled at two developmental stages (gastrula and pluteus)

2013-01-01 | E-GEOD-37522 | biostudies-arrayexpress

Strongylocentrotus purpuratus high resolution developmental transcriptomic time-course

Project description:Classical embryological studies revealed that during mid-embryogenesis vertebrates show similar morphologies. This âphylotypic stageâ has recently received support from transcriptome analyses, which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a âzootypicâ stage, however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum, including a segmented worm, a flatworm, a roundworm, a water bear, a fruitfly, a sea urchin, a zebrafish, a sea anemone, a sponge, and a comb jelly. For each species, we collected the embryonic transcriptomes at ~100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly, we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation, and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes, also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. 165 single embryo samples.

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Strongylocentrotus purpuratus

Project description:Gene expression alterations in SoxC knockdown sea urchin embryos

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Strongylocentrotus purpuratus

Project description:purple sea urchin marine invertebrate used as a model organism to study embryological development and gene regulation

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Single-cell RNA sequencing of the Strongylocentrotus purpuratus larva reveals the blueprint of major cell types and nervous system of a non-chordate deuterostome

Project description:Identifying the molecular fingerprint of organismal cell types is key for understanding their function and evolution. We use single-cell RNA sequencing (scRNA-seq) to survey the cell types of the sea urchin early pluteus larva.

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Nucleosome positioning and sensitivity suggest novel functional organization of the purple sea urchin (Strongylocentrotus purpuratus) genome

Project description:The eukaryotic nucleosome is the fundamental subunit of chromatin and plays functional roles in DNA templated processes including replication and transcription. In eukaryotic promoters, nucleosome organization is generally thought to be highly structured, with nucleosomes occupying canonical positions flanking the transcription start site (TSS), thereby regulating access of the transcriptional machinery to the underlying DNA. We sought to determine whether this canonical distribution is present in the purple sea urchin, Strongylocentrotus purpuratus, an important developmental model organism. We used titrations of micrococcal nuclease to produce high throughput maps of nucleosome distribution, sensitivity to digestion, and subnucleosomal footprints from female urchin gonad tissue. Unlike yeast, flies, zebrafish, maize, or humans, urchins lack a nucleosome depleted region over TSSs. Urchin promoters are dominated by strongly positioned and highly occupied +1 and +2 nucleosomes which are most prominent in highly expressed genes. Additionally, urchin promoters exhibit distinct patterns of sensitivity to nuclease digestion, with heightened sensitivity upstream of the TSS and limited resistance to nuclease digestion. Discretely positioned sensitive nucleosomes were enriched in promoters of highly expressed genes, suggesting a relationship between nucleosome sensitivity and transcriptional regulation. Moreover, urchin promoters were enriched for small fragment-protected footprints associated with known regulatory motifs. Collectively, we present a comprehensive overview of the unique interplay between nucleosome positioning, chromatin sensitivity, cis-regulatory interactions, and gene expression in sea urchins. Our study not only provides a reproducible methodology applicable to other organisms, but also advances our understanding of functional chromatin organization and gene regulation in urchins.

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Project description:A high-resolution transcriptome map of the sea urchin embryo

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