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Items: 1 to 20 of 323

1.

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

(Submitter supplied) Using MethylC-seq we investigated single-base resolution methylomes of sea urchin during development.
Organism:
Strongylocentrotus purpuratus
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL30935
8 Samples
Download data: BED
Series
Accession:
GSE188333
ID:
200188333
2.

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

(Submitter supplied) Using hMeDIP-seq we validated the single-base resolution hydroxymethylomes (ACE-seq) of sea urchin, lancelet and zebrafish embryos.
Organism:
Danio rerio; Branchiostoma lanceolatum; Strongylocentrotus purpuratus
Type:
Methylation profiling by high throughput sequencing
Platforms:
GPL25186 GPL23085 GPL30935
8 Samples
Download data: BW
Series
Accession:
GSE188332
ID:
200188332
3.

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

(Submitter supplied) Using ACE-seq we investigated single-base resolution hydroxymethylomes of sea urchin, lancelet and zebrafish during development.
Organism:
Branchiostoma lanceolatum; Danio rerio; Strongylocentrotus purpuratus
Type:
Other
5 related Platforms
15 Samples
Download data: BED
Series
Accession:
GSE188331
ID:
200188331
4.

Developmental dynamics of sea urchin and sea star cis-regulation and the evolution of echinoderm genome organization

(Submitter supplied) We identified cis-regulatory elements based on their dynamic chromatin accessibility during the gastrula-larva stages of sea urchin and sea star and studied their evolution in these echinoderm species
Organism:
Strongylocentrotus purpuratus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL28450
2 Samples
Download data: BW, NARROWPEAK
Series
Accession:
GSE186363
ID:
200186363
5.

Global patterns of enhancer activity during sea urchin embryogenesis assessed by eRNA profiling

(Submitter supplied) We used CAGE-seq (Capped Analysis of Gene Expression with Sequencing) to profile eRNA expression and enhancer activity during embryogenesis of the sea urchin, Strongylocentrotus purpuratus. We identified >18,000 enhancers that were active during late oogenesis and early development and documented a burst of enhancer activation during cleavage and early blastula stages. Most enhancers were located near gene bodies and eRNA expression levels were highest for elements near core promoters. more...
Organism:
Strongylocentrotus purpuratus
Type:
Expression profiling by high throughput sequencing; Other
Platform:
GPL19892
9 Samples
Download data: BED, BW
Series
Accession:
GSE169227
ID:
200169227
6.

PRO-seq, ATAC-seq, and Pol II ChIP-seq in 20 hour sea urchin embryos (ChIP-seq)

(Submitter supplied) PRO-seq, ATAC-seq, and Pol II ChIP-seq signals are used to predict active developmental enhancers.
Organism:
Strongylocentrotus purpuratus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL20965
6 Samples
Download data: BED, BW
Series
Accession:
GSE160462
ID:
200160462
7.

PRO-seq, ATAC-seq, and Pol II ChIP-seq in 20 hour sea urchin embryos (ATAC-Seq)

(Submitter supplied) PRO-seq, ATAC-seq, and Pol II ChIP-seq signals are used to predict active developmental enhancers.
Organism:
Strongylocentrotus purpuratus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL20965
5 Samples
Download data: BED, BIGWIG, BW, NARROWPEAK
Series
Accession:
GSE160461
ID:
200160461
8.

PRO-seq, ATAC-seq, and Pol II ChIP-seq in 20 hour sea urchin embryos (PRO-Seq)

(Submitter supplied) PRO-seq, ATAC-seq, and Pol II ChIP-seq signals are used to predict active developmental enhancers.
Organism:
Strongylocentrotus purpuratus
Type:
Other
Platform:
GPL20965
10 Samples
Download data: BED, BW
9.

Regulation of dynamic pigment cell states at single-cell resolution

(Submitter supplied) Pigment cells bear molecules with diverse physiological roles across phylogeny and are often under strict evolutionary selection. Thus, the mechanisms of regulating these cells, and the pigments within them, are of critical importance. Here, we explore the regulation of pigment cells in the purple sea urchin Strongylocentrotus purpuratus, an emerging model for understudied pigments at a molecular level. more...
Organism:
Strongylocentrotus purpuratus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL28450
4 Samples
Download data: MTX, RDS, TSV
Series
Accession:
GSE155427
ID:
200155427
10.

A single cell RNA-seq resource for early sea urchin development

(Submitter supplied) Here we leverage the sea urchin embryo for its rich history of developmental transitions, its well-established gene regulatory network, and the ability to readily dissociate embryos into single cells to interrogate the embryo by single cell RNA-seq. We tested eight developmental stages in S. purpuratus, from the eight-cell stage to late in gastrulation. The analysis revealed cell types derived from the abundant cells of the three germ layers as well as the rare cells of the germline. more...
Organism:
Strongylocentrotus purpuratus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL28450
8 Samples
Download data: MTX, RDS, TSV
Series
Accession:
GSE149221
ID:
200149221
11.

The evolution of DNA methylation inheritance and programming in animals

(Submitter supplied) DNA methylation has been found throughout animal kingdom, but it is still unclear whether this epigenetic mechanism affects the evolution of genomic elements in animals. Here, we compare the DNA methylomes of gametes and embryos from 7 representative animal species. We find that parental methylomes are propagated to the progeny without significant changes during embryogenesis in cnidarians and insects, but undergo substantial reprogramming in echinoderms, and the reprogramming become more dramatic during deuterostome evolution. more...
Organism:
Nematostella vectensis; Apis mellifera; Ciona savignyi; Strongylocentrotus purpuratus
Type:
Methylation profiling by high throughput sequencing
4 related Platforms
22 Samples
Download data: BED
Series
Accession:
GSE73545
ID:
200073545
12.

Single cell RNA‐seq in the sea urchin embryo show marked cell‐type specificity in the Delta/Notch pathway

(Submitter supplied) Overall, we conclude that single cell RNA‐seq analysis in this embryo is revealing of the cell types present during development, of the changes in the gene regulatory network resulting from inhibition of various signaling pathways, and of the selectivity of these pathways in influencing developmental trajectories.
Organism:
Strongylocentrotus purpuratus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20965
3 Samples
Download data: TXT
Series
Accession:
GSE134350
ID:
200134350
13.

Genome-wide identification of binding sites and gene targets of Alx1, a pivotal regulator of echinoderm skeletogenesis

(Submitter supplied) ChIP-seq provides a genome-wide view of the binding sites of Alx1, a pivotal transcription factor in a gene regulatory network that controls skeletogenesis in sea urchins and other echinoderms.
Organism:
Strongylocentrotus purpuratus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL20965
2 Samples
Download data: BED, NARROWPEAK
Series
Accession:
GSE131370
ID:
200131370
14.

Chromatin accessibility profiling identifies cis-regulatory modules in an early embryonic cell lineage

(Submitter supplied) We used DNase-seq and ATAC-seq to identify a set of putative CRMs regulating skeletogenic gene expression during sea urchin embryogenesis. These CRMs, identified by differential chromatin accessibility, are likely to be regulated by two upstream TFs, Alx1 and Ets1, that are part of the skeletogenic GRN. 9/31 od these identified CRMs were validated by reporter gene assay. Our work demonstrates the value of using differential chromatin accessibility for the high-throughput identification of CRMs in embryonic tissues.
Organism:
Strongylocentrotus purpuratus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL23218 GPL19892
10 Samples
Download data: BED, TXT
Series
Accession:
GSE96927
ID:
200096927
15.

Evolutionary recruitment of flexible Esrp-dependent splicing programs into diverse embryonic morphogenetic processes

(Submitter supplied) Epithelial-mesenchymal interactions are crucial for the development of multiple animal structures. Thus, unraveling how molecular tools are recruited in different lineages to control the interplay between these tissue types is key to understand morphogenetic evolution. Here, we studied Epithelial Splicing Regulatory Protein (Esrp) genes, which regulate extensive alternative splicing programs associated with cell adhesion and motility in human cells and are essential during mouse organogenesis. more...
Organism:
Strongylocentrotus purpuratus; Danio rerio
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL20965 GPL18413
8 Samples
Download data: TXT
Series
Accession:
GSE97267
ID:
200097267
16.

Gene expression in tissues from an immune challenged adult sea urchin (Strongylocentrotus purpuratus)

(Submitter supplied) To induce an immune response, a single adult animal was injected intracoelomically with complex microbiota isolated from the gut of another adult animal (4.8 × 10^6 total bacteria). After 12 hours, phagocytic coelomocytes and gut tissue were collected for RNA-Seq experiments.
Organism:
Strongylocentrotus purpuratus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23220
2 Samples
Download data: TXT
Series
Accession:
GSE97448
ID:
200097448
17.

The sea urchin larval response to immune challenge with Vibrio diazotrophicus

(Submitter supplied) Seawater exposure to the gram negative marine bacterium Vibrio diazotrophicus induces a robust cellular response in sea urchin larvae that includes the migration of pigment cells to the gut epithelium, changes in cell behavior and altered gut morphology (Ho et al., 2016; PMID 27192936). To investigate the transcriptional underpinnings of this response, whole transcriptome sequencing was performed on mRNA isolated from larval samples collected at 0, 6, 12 and 24 hr of exposure to V. more...
Organism:
Strongylocentrotus purpuratus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23220
4 Samples
Download data: TXT
Series
Accession:
GSE96940
ID:
200096940
18.

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

(Submitter supplied) We have adapted ATAC-seq to sea urchin embryos. As a proof of concept, we documented strong ATAC-seq signals over the locations of a number of previously authenticated, developmentally active, cell type specific cis-regulatory modules. We then used the method to generate a systematic developmental series for embryos from three independent batches, obtained every six hours from blastula stage until completion of embryogenesis at 72h. more...
Organism:
Strongylocentrotus purpuratus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL20965
21 Samples
Download data: BED
Series
Accession:
GSE95651
ID:
200095651
19.

Genome-wide detection of Tbrain binding sites during early development in both sea urchin (S. purpuratus) and sea star (P. miniata)

(Submitter supplied) Sea stars and sea urchins are model systems for interrogating the types of deep evolutionary changes that have restructured developmental gene regulatory networks (GRNs). While cis regulatory DNA evolution is likely the predominant mechanism of change, it was recently shown that Tbrain, a Tbox transcription factor protein, has evolved a changed preference for a low affinity, secondary binding motif, although the primary, high affinity motif is conserved. more...
Organism:
Strongylocentrotus purpuratus; Patiria miniata
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL20965 GPL22676
4 Samples
Download data: BED, BEDGRAPH
Series
Accession:
GSE89862
ID:
200089862
20.

Strongylocentrotus purpuratus high resolution developmental transcriptomic time-course

(Submitter supplied) Classical embryological studies revealed that during mid-embryogenesis vertebrates show similar morphologies. This “phylotypic stage” 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. more...
Organism:
Strongylocentrotus purpuratus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19892
165 Samples
Download data: TAB
Series
Accession:
GSE70372
ID:
200070372
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