GEO DataSets

(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

(Submitter supplied) To explore the evolution of different cell types across species, we compared transcriptomes between different cell types between two echinoderm species, P. miniata and S. purpuratus. snRNA-seq was used to analyze to characterize diffente cell states. For each species, the time points were integrated into a common atlas and annotated. The fully processed and annotated P. miniata and S. purpuratus atlases are available as supplementary files.

Organism:

Strongylocentrotus purpuratus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29871

4 Samples

Download data: MTX, RDS, TSV

(Submitter supplied) To explore the evolution of different cell types across species, we compared transcriptomes between different cell types between two echinoderm species, P. miniata and S. purpuratus. snRNA-seq was used to analyze to characterize diffente cell states. For each species, the time points were integrated into a common atlas and annotated. The fully processed and annotated P. miniata and S. purpuratus atlases are available as supplementary files.

Organism:

Patiria miniata

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33652

3 Samples

Download data: MTX, RDS, TSV

(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

(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

(Submitter supplied) Identifying the molecular fingerprint of organismal cell types is key for understanding their function and evolution. We use single-cell RNA sequencing (scRNA-seq) to survey the cell types of the sea urchin early pluteus larva.

Organism:

Strongylocentrotus purpuratus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23218

6 Samples

Download data: RDS

(Submitter supplied) The sea urchin S. purpuratus is a model organism for study of the genomic control circuitry underlying embryonic development. We examined the complete repertoire of genes expressed in the S. purpuratus embryo, up to late gastrula stage, by means of high-resolution custom tiling arrays covering the whole genome. We detected complete spliced structures even for genes known to be expressed at low leveles in only a few cells. more...

Organism:

Strongylocentrotus purpuratus

Type:

Expression profiling by genome tiling array

27 related Platforms

27 Samples

Download data

(Submitter supplied) Stress responses play an important role in shaping species distributions and robustness to climate change. We investigated how stress responses alter the contribution of additive genetic variation to gene expression during development of the purple sea urchin, Strongylocentrotus purpuratus, under increased temperatures that model realistic climate change scenarios. We first measured gene expression responses in the embryos by RNA-seq to characterize molecular signatures of mild, chronic temperature stress in an unbiased manner. more...

Organism:

Strongylocentrotus purpuratus

Type:

Expression profiling by array

Platform:

GPL13644

191 Samples

Download data: TXT

(Submitter supplied) Stress responses play an important role in shaping species distributions and robustness to climate change. We investigated how stress responses alter the contribution of additive genetic variation to gene expression during development of the purple sea urchin, Strongylocentrotus purpuratus, under increased temperatures that model realistic climate change scenarios. We first measured gene expression responses in the embryos by RNA-seq to characterize molecular signatures of mild, chronic temperature stress in an unbiased manner. more...

Organism:

Strongylocentrotus purpuratus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15679

7 Samples

Download data: TXT

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

Organism:

Strongylocentrotus purpuratus

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL13644 GPL15679

198 Samples

Download data: TXT

(Submitter supplied) microRNAs (miRNAs) are small noncoding RNAs that mediate post-transcriptional gene regulation and have emerged as essential regulators of many developmental events. The transcriptional network during early embryogenesis of the purple sea urchin, Strongylocentrotus purpuratus, is well described and would serve as an excellent model to test functional contributions of miRNAs in embryogenesis. We examined the loss of function phenotypes of the major components of the miRNA biogenesis pathway. more...

Organism:

Strongylocentrotus purpuratus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15247

6 Samples

Download data: TSV

(Submitter supplied) The goal of this gene expression profiling experiment was to identify the entire set of transcription factors expressed during late pupal wing development (~80h APF) when pigmentation genes are expressed

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL1322

3 Samples

Download data: CEL

(Submitter supplied) In this research we present a transcriptomics analysis of the physiological response of a marine calcifier, Strongylocentrotus purpuratus, to ocean acidification, a decline in ocean pH that results from the absorption of anthropogenic carbon dioxide (CO2). Larvae were raised from fertilization to prism stage in seawater with elevated CO2 conditions based upon IPCC emissions scenario B1 (540ppm CO2) and A1FI (1020ppm CO2).

Organism:

Strongylocentrotus purpuratus

Type:

Expression profiling by array

Platform:

GPL7011

12 Samples

Download data: GPR