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Items: 1 to 20 of 946

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; Saccharomyces cerevisiae; Drosophila melanogaster; Gallus gallus; Hypsibius dujardini; Lethenteron camtschaticum; Arachis hypogaea; Agaricus bisporus; Branchiostoma lanceolatum; Xenopus laevis; Notamacropus eugenii; Pygocentrus nattereri; Cristatella mucedo; Clonorchis sinensis; Chiloscyllium punctatum; 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.

Transcriptomic Analysis of Early Stages of Intestinal Regeneration in Holothuria glaberrima

(Submitter supplied) We assembled and annotated a de novo transcriptome using RNA-seq data consisting of regenerating and non-regenerating intestinal tissues from the sea cucumber Holothuria glaberrima. Analysis of differential expression revealed a large number of differentially expressed transcripts associated with transcription factors with diverse expression patterns. Activity involving developmental and cancer-related events found in the analysis could be related to the regenerative process. more...
Organism:
Holothuria glaberrima
Type:
Expression profiling by high throughput sequencing
Platform:
GPL29317
9 Samples
Download data: CSV, FASTA, XLSX
Series
Accession:
GSE160340
ID:
200160340
8.

The sea urchin larval response to metaloxide nanoparticule exposure

(Submitter supplied) Engineered nanoparticles (ENPs) are increasingly used to generate innovative industrial and medical goods. Because of their broad applications, they form a new class of pollutants with potential eco-toxicological impacts on marine ecosystems. Attempting to evaluate the risk, we investigated the toxicity of Iron and Zinc oxide ENPs on Paracentrotus lividus sea urchin embryos. Sea urchin embryos are sensitive to both ENPs with a much stronger impact of ZnO ENPs. more...
Organism:
Paracentrotus lividus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL27788
19 Samples
Download data: CSV, FA
Series
Accession:
GSE140784
ID:
200140784
9.

Transcriptomic analysis of the body wall of farmed sea cucumber Isostichopus badionotus specimens

(Submitter supplied) These data corresponds to RNA-Seq assays obtained from the body wall of farmed I. badionotus juveniles samples. These raw reads were used to evaluate differential gene expression between wild and farmed Isostichopus badionotus specimens. With this aim, a de-novo transcriptome assembled from wild specimens was used as reference. Further information about de-novo assembled transcriptome is available within the BioProject PRJNA639785.
Organism:
Isostichopus badionotus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL29088
6 Samples
Download data: FA, TXT
Series
Accession:
GSE157183
ID:
200157183
10.

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
11.

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
12.

Age-related gene expression in tissues of the long-lived red sea urchin

(Submitter supplied) The red sea urchin, Mesocentrotus franciscanus, is one the earth’s longest-lived animals, reported to live more than 100 years with indeterminate growth, life-long reproduction and no increase in mortality rate with age. To explore the idea that transcriptional stability is a key determinant of longevity and negligible senescence, age-related gene expression was examined in three tissues of the red sea urchin (Aristotle’s lantern muscle, esophagus and radial nerve cord). more...
Organism:
Mesocentrotus franciscanus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL27148
18 Samples
Download data: FASTA, TXT
Series
Accession:
GSE136352
ID:
200136352
13.

Understanding microRNAs regulation in heat shock response in the sea cucumber Apostichopus japonicus

(Submitter supplied) In this study, we sought to determine the expression profiles of miRNAs under HS in A. japonicus by using HiSeq techinique. Nine miRNA libraries of sea cucumbers (Control: C1, C2, C3; HS 6h: 6h1, 6h2, 6h3; HS 48h: 48h1, 48h2, 48h3 ) were sequenced respectively. We highlighted differentially expressed miRNAs among HS groups, many of which were invovled of immunity process and disease regulation.
Organism:
Apostichopus japonicus
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL23583
9 Samples
Download data: FA, XLSX
Series
Accession:
GSE115076
ID:
200115076
14.

Integrated analysis of sea cucumber ambient temperature and dissolved oxygen responsive lncRNAs and mRNAs

(Submitter supplied) In this work, identification of differentially expressed (DE) genes, including lncRNAs and mRNAs, in sea cucumber response to multiple environmental stress, such as thermal, hypoxic and the combined treatment.
Organism:
Apostichopus japonicus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL25856
12 Samples
Download data: TXT
Series
Accession:
GSE131676
ID:
200131676
15.

An Initial Comparative Genomic Autopsy of Wasting Disease in Sea Stars

(Submitter supplied) Beginning in 2013, sea stars throughout the Eastern North Pacific were decimated by wasting disease, also known as ‘asteroid idiopathic wasting syndrome’ (AIWS) due to its elusive etiology. The geographic extent and taxonomic scale of AIWS meant events leading up to the outbreak were heterogeneous, multifaceted, and oftentimes unobserved; progression from morbidity to death was rapid, leaving few tell-tale symptoms. more...
Organism:
Pisaster ochraceus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL28087
50 Samples
Download data: TXT
Series
Accession:
GSE144422
ID:
200144422
16.

Active Notch Signaling is Required for Arm Regeneration ina Brittle Star

(Submitter supplied) Cell signaling pathways play key roles to coordinate cellular events in development. Notch signaling pathway is highly conserved across all multicellular animals and is known to co- ordinate a multitude of diverse cellular events, including proliferation, differentiation, fate specification, and cell death. Specific functions of the pathway are however highly context- dependent and are not well characterized in post-traumatic regeneration. more...
Organism:
Ophioderma brevispina
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL27936 GPL27935
7 Samples
Download data: FASTA, TXT
Series
Accession:
GSE142391
ID:
200142391
17.

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
18.

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
19.

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
20.

Transcriptome landscape during tenderization in sea cucumber Apostichopus japonicus

(Submitter supplied) The gene expression profiles associated with tenderization in body wall of sea cucumber (Apostichopus japonicus) were determined
Organism:
Apostichopus japonicus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL25856
9 Samples
Download data: FA, TXT
Series
Accession:
GSE123077
ID:
200123077
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db=gds|term=txid7586[Organism:exp]|query=1|qty=48|blobid=MCID_6100377f5def9a15542b9b80|ismultiple=true|min_list=5|max_list=20|def_tree=20|def_list=|def_view=|url=/Taxonomy/backend/subset.cgi?|trace_url=/stat?
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