Format
Items per page
Sort by

Send to:

Choose Destination

Search results

Items: 1 to 20 of 695

1.

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
2.

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
3.

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
4.

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
5.

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
6.

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
7.

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
8.

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
9.

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
10.

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
11.

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
12.

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
13.

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
14.

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
15.

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
16.

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
17.

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
18.

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
19.

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
20.

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
Format
Items per page
Sort by

Send to:

Choose Destination

Supplemental Content

db=gds|term=txid7586[Organism:exp]|query=1|qty=17|blobid=NCID_1_88146599_130.14.18.34_9001_1534893895_1646478833_0MetA0_S_MegaStore_F_1|ismultiple=true|min_list=5|max_list=20|def_tree=20|def_list=|def_view=|url=/Taxonomy/backend/subset.cgi?|trace_url=/stat?
   Taxonomic Groups  [List]
Tree placeholder
    Top Organisms  [Tree]

Find related data

Search details

See more...

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...
Support Center