txid7586[Organism:exp] - GEO DataSets

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Select item 2000969271.

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

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000972672.

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

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001034663.

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

PubMed Similar studies SRA Run Selector

Select item 2000872104.

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

SRA Run Selector

Select item 2001006035.

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

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000974486.

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

SRA Run Selector

Select item 2000969407.

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

SRA Run Selector

Select item 2000956518.

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

SRA Run Selector

Select item 2000898659.

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

PubMed Full text in PMC Similar studies

Select item 20008986310.

RNA-seq assessment of morpholino knockdown of the sea star (Patiria miniata) Pm-Tbr transcription factor in early embryos

(Submitter supplied) Purpose: The Tbrain transcription factor has demonstrated an evolved preference for low-affinity, secondary site binding motifs between the sea star and sea urchin orthologs. We sought to identify targets of sea urchin and sea star orthologs of Tbr. Because less is known about the function of Tbr during sea star development, we used RNA-seq in conjuction with ChIP-seq studies (GEO:xxxx) to determine the targets of sea star Tbr in early development. more...

Organism:: Patiria miniata

Type:: Expression profiling by high throughput sequencing

Platform:: GPL22676
6 Samples

Download data: TXT

Series

Accession:: GSE89863

ID:: 200089863

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20008986211.

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

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20008780312.

Differential gene expression in the body wall of the sea cucumber (Apostichopus japonicus) under strong lighting and dark conditions

(Submitter supplied) RNA-seq provided a general overview of the gene expression profiles of the body walls of A. japonicus exposed to strong light (“light”), normal light (“control”) and fully dark (“dark”) environment.

Organism:: Apostichopus japonicus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL16771
3 Samples

Download data: TXT

Series

Accession:: GSE87803

ID:: 200087803

SRA Run Selector

Select item 20005381513.

Gene expression profiles of the respiratory tree of sea cucumber Apostichopus japonicus during aestivation by RNA-seq

(Submitter supplied) Sea cucumbers (Holothuroidea; Echinodermata) cycle annually between aestivation, when water temperature is above about 25°C in the summer, and active life, when temperature is below about 18°C. We used RNA-Seq to determine gene expression profiles of respiratory tree tissue of A. japonicus during non-aestivation (NA), deep-aestivation (DA), and arousal from aestivation (AA).

Organism:: Apostichopus japonicus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL16771
3 Samples

Download data: TXT

Series

Accession:: GSE53815

ID:: 200053815

PubMed Similar studies SRA Run Selector

Select item 20008001214.

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

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20007018515.

The mid-developmental transition and the evolution of animal body plans

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Danio rerio; Mnemiopsis leidyi; Nematostella vectensis; Schmidtea polychroa; Hypsibius dujardini; Platynereis dumerilii; Drosophila melanogaster; Amphimedon queenslandica; Caenorhabditis elegans; Strongylocentrotus purpuratus

Type:: Expression profiling by high throughput sequencing

10 related Platforms
1143 Samples

Download data: PDF, XLSX

Series

Accession:: GSE70185

ID:: 200070185

PubMed Full text in PMC Similar studies

Select item 20007037216.

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

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20007606717.

Gene expression alterations in SoxC knockdown sea urchin embryos

(Submitter supplied) Transcription factor SoxC is required for all neural development in purple sea urchin S. purpuratus embryos. To begin to develop a gene regulatory network for neural development, we used RNA-Seq to compare transcript populations in SoxC knockdown and control embryos.

Organism:: Strongylocentrotus purpuratus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL19892
2 Samples

Download data: TXT

Series

Accession:: GSE76067

ID:: 200076067

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20005113718.

RNA-Seq dependent transcriptional analysis unveils adaptive mechanisms in the intestine of sea cucumber Apostichopus japonicus during aestivation

(Submitter supplied) Sea cucumbers (Holothuroidea; Echinodermata), cycle annually between aestivation when water temperature is above about 25°C in the summer and active life when temperature is below about 18°C. We used RNA-Seq to determine gene expression profiles of intestine tissue of A.japonicus during non-aestivation (NA), deep-aestivation (DA), and arousal from aestivation (AA).

Organism:: Apostichopus japonicus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL16771
3 Samples

Download data: TXT

Series

Accession:: GSE51137

ID:: 200051137

PubMed Similar studies SRA Run Selector

Select item 20006690019.

Evolutionary comparison reveals that diverging CCCTC-binding factor (CTCF) sites are signatures of ancestral topological associating domains borders

(Submitter supplied) Comparison of conserved TAD boundaries reveals that diverging CTCF sites is an evolutionary conserved signature associated with TAD borders

Organism:: Mus musculus; Danio rerio; Strongylocentrotus purpuratus

Type:: Other

Platforms:: GPL19892 GPL13112 GPL14875
63 Samples

Download data: BEDGRAPH

Series

Accession:: GSE66900

ID:: 200066900

PubMed Full text in PMC Similar studies Analyze with GEO2R SRA Run Selector

Select item 20004499520.

NA-Seq reveals dynamic changes of gene expression in key stages of intestine regeneration in the sea cucumber Apostichopus japonicus.

(Submitter supplied) Sea cucumbers (Holothuroidea; Echinodermata) have the capacity to regenerate lost tissues and organs.We used RNA-Seq to determine gene expression profiles associated with intestinal regeneration in A. japonicus at 3, 7, 14 and 21 days post evisceration (dpe)

Organism:: Apostichopus japonicus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL16771
5 Samples

Download data: FNA, TXT

Series

Accession:: GSE44995

ID:: 200044995

PubMed Full text in PMC Similar studies SRA Run Selector

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