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Items: 1 to 20 of 863

1.

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
2.

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
3.

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
4.

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
5.

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
6.

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:
GPL27935 GPL27936
7 Samples
Download data: FASTA, TXT
Series
Accession:
GSE142391
ID:
200142391
7.

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; Strongylocentrotus purpuratus; Apis mellifera; Ciona savignyi
Type:
Methylation profiling by high throughput sequencing
4 related Platforms
22 Samples
Download data: BED
Series
Accession:
GSE73545
ID:
200073545
8.

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
9.

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
10.

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
11.

Differential expression of genes in the respiratory tree of sea cucumber (Apostichopus japonicus) under normal dissolved oxygen and hypoxia conditions

(Submitter supplied) The sea cucumber Apostichopus japonicus is a deposit-feeder and vital for marine benthic ecosystems. Hypoxia lasting for several days can lead to massive mortality in A. japonicus. It is important to understand the molecular responses of A. japonicus when exposed to acute changes in DO concentration. In the present study, RNA-seq provided a general overview of the gene expression profiles of the respiratory tree of A. more...
Organism:
Apostichopus japonicus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23583
9 Samples
Download data: XLS
Series
Accession:
GSE100042
ID:
200100042
12.

Regeneration time course of a larval sea star, Patiria miniata

(Submitter supplied) Regeneration is pervasive among the metazoa, but to vastly varying degrees. Platyhelminthes, Cnidaria, and Echinodermata are examples of phyla whose members are capable of whole-body regeneration (WBR). While planaria and hydra have been exemplary models of this phenomenon, the molecular details of echinoderm WBR are less established. It remains unclear to what degree such a dramatic regenerative capacity is due to the operation of conserved mechanisms and, in particular, whether any of these are involved in a regenerating Deuterostome. more...
Organism:
Patiria miniata
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL23240 GPL22676
18 Samples
Download data: GTF, TXT
Series
Accession:
GSE97230
ID:
200097230
13.

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
14.

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
15.

Differential gene expression in the intestine of sea cucumber (Apostichopus japonicus) under low and high salinity conditions

(Submitter supplied) Sea cucumber, Apostichopus japonicus is a very important species for aquaculture, and its behavior and physiology can respond to the initial change in salinity. It is important to understand the molecular responses of A. japonicus when exposed to ambient changes in salinity In this study, RNA-seq provided a general overview of the gene expression profiles of the intestine of A. japonicus exposed to high salinity (SD40), normal salinity (SD30) and low salinity (SD20) environment.
Organism:
Apostichopus japonicus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23583
9 Samples
Download data: FASTA, TXT
Series
Accession:
GSE103466
ID:
200103466
16.

High-throughput Sequencing Reveals Differential expression of MicroRNAs during intestine regeneration of sea cucumber Apostichopus japonicus

(Submitter supplied) We applied high-throughput sequencing to investigate the alterations of miRNAs expression in regenerative intestine (3dpeA, 3dpeB, 3dpeC) Vs normal intestine (ControlA, ControlB, ControlC).
Organism:
Apostichopus japonicus
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL16771
6 Samples
Download data: TXT
Series
Accession:
GSE87210
ID:
200087210
17.

High-Throughput Sequencing Reveals Differential Expression of miRNAs in respiratory tree from the sea cucumber Apostichopus japonicus Under Hypoxia Stress

(Submitter supplied) The present study identified and characterized miRNAs, which may play a major role in stress resistance. we applied high-throughput sequencing to investigate the alterations of miRNAs expression of sea cucumber under hypoxia stress(DO2_1,DO2_2,DO2_3),slight hypoxia stress(DO4_1,DO4_2,DO4_3) and normal condition(DO8_1,DO8_2,DO8_3). These results will provide a basis for future studies of miRNA regulation in sea cucumbers under hypoxia stress.
Organism:
Apostichopus japonicus
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL23638
9 Samples
Download data: XLSX
Series
Accession:
GSE100603
ID:
200100603
18.

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
19.

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
20.

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
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