Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Strongylocentrotus purpuratus

ABSTRACT: Whole genome developmental time course of Tn5 transposon accessible chromatin patterns in sea urchin embryos

PROVIDER: PRJNA377768 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR5310900_1.fastq.gz	Fastqsanger.gz
	SRR5310900_2.fastq.gz	Fastqsanger.gz
	SRR5310910_1.fastq.gz	Fastqsanger.gz
	SRR5310910_2.fastq.gz	Fastqsanger.gz
	SRR5310901_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 40

Similar Datasets

Strongylocentrotus purpuratus

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

| PRJNA306145 | ENA

Strongylocentrotus purpuratus

Project description:Strongylocentrotus purpuratus high resolution developmental transcriptomic time-course

| PRJNA288459 | ENA

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

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.

2025-05-05 | GSE283453 | GEO

DNA hydroxymethylation profiling of purple sea urchin (Strongylocentrotus purpuratus), european lancelet (Branchiostoma lanceolatum) and zebrafish (Danio rerio) using hMeDIP-seq

Project description:Using hMeDIP-seq we validated the single-base resolution hydroxymethylomes (ACE-seq) of sea urchin, lancelet and zebrafish embryos.

2021-11-08 | GSE188332 | GEO

Response to elevated pCO2 in Strongylocentrotus purpuratus larvae

2013-01-01 | GSE37522 | GEO

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.

2021-11-08 | GSE188333 | GEO

Phosphoproteomic Network Analysis in the Sea Urchin Strongylocentrotus purpuratus Reveals New Candidates in Egg Activation

Project description:Fertilization triggers a dynamic symphony of molecular transformations induced by a rapid rise in intracellular calcium. Most prominent are surface alterations, metabolic activation, cytoskeletal reorganization, and cell cycle reentry. While the activation process appears to be broadly evolutionarily conserved, and protein phosphorylation is known to play a key role, the signaling networks mediating the response to fertilization are not well described. To address this gap, we performed a time course phosphoproteomic analysis of egg activation in the sea urchin Strongylocentrotus purpuratus, a system that offers biochemical tractability coupled with exquisite synchronicity. By coupling large-scale phosphopeptide enrichment with unbiased quantitative mass spectrometry, we identified striking changes in global phosphoprotein patterns at 2- and 5- min post fertilization as compared to unfertilized eggs. Overall, we mapped 8796 distinct phosphosite modifications on 2833 phosphoproteins, of which 15% were differentially regulated in early egg activation. Activated kinases were identified by phosphosite mapping, while enrichment analyses revealed conserved signaling cascades not previously associated with egg activation. This work represents the most comprehensive study of signaling associated with egg activation to date, providing both novel mechanistic insights and a valuable resource for the broader research community.

2015-08-04 | PXD002239 | Pride

Strongylocentrotus purpuratus

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

| PRJNA97757 | ENA

Strongylocentrotus purpuratus

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

| PRJNA151931 | ENA