txid7586[Organism:exp] - GEO DataSets

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Select item 2001692271.

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

Analyze with GEO2R SRA Run Selector

Select item 2001604632.

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

Analyze with GEO2R

Select item 2001604623.

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

SRA Run Selector

Select item 2001604614.

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

SRA Run Selector

Select item 2001604605.

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

Analyze with GEO2R SRA Run Selector

Select item 2001690886.

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

Select item 2001603407.

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

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001407848.

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

PubMed Similar studies SRA Run Selector

Select item 2001571839.

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

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20015542710.

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

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20014922111.

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

PubMed Similar studies SRA Run Selector

Select item 20013635212.

(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

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20011507613.

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

SRA Run Selector

Select item 20013167614.

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

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20014442215.

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

PubMed Similar studies SRA Run Selector

Select item 20014239116.

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

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20007354517.

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

SRA Run Selector

Select item 20013435018.

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

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20013137019.

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.