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Items: 1 to 20 of 653

1.

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
2.

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

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Strongylocentrotus purpuratus
Type:
Other; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL20965
21 Samples
Download data: BIGWIG, BW, NARROWPEAK
Series
Accession:
GSE160463
ID:
200160463
3.

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
4.

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
5.

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
Series
Accession:
GSE160460
ID:
200160460
6.

3D genomics across the tree of life reveals condensin II as a determinant of architecture type

(Submitter supplied) We investigated genome folding across the eukaryotic tree of life. We find four general manifestations of genome organization at chromosome-scale that each emerge and disappear repeatedly over the course of evolution. The submission represents chromosome-length Hi-C contact maps, architecture type and homolog separation analyses for 26 species across the tree of life, representing all subphyla of chordates, all 7 extant vertebrate classes, and 7 out of 9 major animal phyla, as well as plants and fungi.
Organism:
Triticum aestivum; Caenorhabditis elegans; Aplysia californica; Aedes aegypti; Culex quinquefasciatus; Homo sapiens; Muntiacus reevesi; Muntiacus muntjak; Arachis hypogaea; Agaricus bisporus; Branchiostoma lanceolatum; Xenopus laevis; Notamacropus eugenii; Pygocentrus nattereri; Cristatella mucedo; Clonorchis sinensis; Chiloscyllium punctatum; Saccharomyces cerevisiae; Drosophila melanogaster; Gallus gallus; Hypsibius dujardini; Lethenteron camtschaticum; Strongylocentrotus purpuratus; Ciona intestinalis; Pleurobrachia bachei; Acropora millepora; Python bivittatus
Type:
Other
30 related Platforms
32 Samples
Download data: BEDPE, FASTA, HIC, VCF, WIG
Series
Accession:
GSE169088
ID:
200169088
7.

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
8.

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
9.

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:
Apis mellifera; Ciona savignyi; Strongylocentrotus purpuratus; Nematostella vectensis
Type:
Methylation profiling by high throughput sequencing
4 related Platforms
22 Samples
Download data: BED
Series
Accession:
GSE73545
ID:
200073545
10.

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
11.

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
12.

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
13.

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:
Danio rerio; Strongylocentrotus purpuratus
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL20965 GPL18413
8 Samples
Download data: TXT
Series
Accession:
GSE97267
ID:
200097267
14.

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
15.

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
16.

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
17.

Genome-wide use of high and low affinity Tbrain transcription factor binding sites during echinoderm development

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Strongylocentrotus purpuratus; Patiria miniata
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL22676 GPL20965
10 Samples
Download data: BED, BEDGRAPH, TXT
Series
Accession:
GSE89865
ID:
200089865
18.

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
19.

Gene expression alteration in FoxQ2 knockdown sea uchin embryos

(Submitter supplied) The transcription factor FoxQ2 is required for anterior pole neural development in S. purpuratus embryos. To understand the gene regulatory network driving neurogenesis in the anterrior pole region, it is necessary to identify genes that depend on FoxQ2. We carried out a microarray experiment to compare gene expression changes in FoxQ2 knockdown embryos.
Organism:
Strongylocentrotus purpuratus
Type:
Expression profiling by array
Platform:
GPL21701
2 Samples
Download data: PAIR, TXT
Series
Accession:
GSE80012
ID:
200080012
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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