Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Widespread priming of transcriptional regulatory elements by incipient accessibility or Pol II pause in early embryos of the sea urchin Strongylocentrotus purpuratus

ABSTRACT: Widespread priming of transcriptional regulatory elements by incipient accessibility or Pol II pause in early embryos of the sea urchin Strongylocentrotus purpuratus

PROVIDER: PRJNA980187 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR24828573_1.fastq.gz	Fastqsanger.gz
	SRR24828573_2.fastq.gz	Fastqsanger.gz
	SRR24828574_1.fastq.gz	Fastqsanger.gz
	SRR24828574_2.fastq.gz	Fastqsanger.gz
	SRR24828575_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 54

Similar Datasets

Response to elevated pCO2 in Strongylocentrotus purpuratus larvae

2013-01-01 | GSE37522 | GEO

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

Synergistic effects of temperature and pCO2 on growth, development and gene expression of Strongylocentrotus purpuratus larvae

Project description:Transcriptional profiling of purple sea urchin (Strongylocentrotus purpuratus) larvae cultured under four different seawater conditions: (i)13°C/400 µatm pCO2, (ii)13°C/1100 µatm pCO2, (iii)18°C/400 µatm pCO2 (iv)18°C/1100 µatm pCO2. The goal was to determine the effects of temperature and CO2, both important climate change variables, on gene expression

2013-01-01 | GSE39125 | 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

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

Strongylocentrotus purpuratus

Project description:Strongylocentrotus purpuratus RNAseq

| PRJNA322662 | ENA

Strongylocentrotus purpuratus

Project description:Strongylocentrotus purpuratus Genomic Resources

| PRJNA808377 | ENA

Strongylocentrotus purpuratus

Project description:Strongylocentrotus purpuratus early transcriptome

| PRJNA531297 | ENA

Strongylocentrotus purpuratus

Project description:Strongylocentrotus purpuratus developmental transcriptomes