GEO DataSets

(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) 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) Transcriptional profiling of purple sea urchin (Strongylocentrotus purpuratus) larvae cultured under four different seawater conditions: (i)13°C/400 µatm pCO2, (ii)13°C/1100 µatm pCO2, (iii)18°C/400 µatm pCO2 (iv)18°C/1100 µatm pCO2. The goal was to determine the effects of temperature and CO2, both important climate change variables, on gene expression

Organism:

Strongylocentrotus purpuratus

Type:

Expression profiling by array

Platform:

GPL15767

12 Samples

Download data: TXT

(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

(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) 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

(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) 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

(Submitter supplied) Sea urchin larvae possess a group of photoreceptor cells (PRCs) deploying a Go-Opsin (Opsin3.2). In this study, we investigate investigate the molecular signature of the Sp-Opsin3.2 cells using single cell transcriptomics.

Organism:

Strongylocentrotus purpuratus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23218

2 Samples

Download data: RDS

(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) Molecular profiles of neurons influence information processing, but bridging the gap between genes, circuits and behavior has been very difficult. Furthermore, the behavioral state of an animal continuously changes across development and as a result of sensory experience. How behavioral state influences molecular cell state is poorly understood. Here we present a complete atlas of the Drosophila larval nervous system. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13304

34 Samples

Download data: GTF, MTX, TSV

(Submitter supplied) Evolutionary transitions enable the wide diversity in life histories of plants and animals. This is particularly germane in the development of the germline in which fitness is a direct readout of evolutionary change. Here, we focused on two distinct sea urchin species who shared a common ancestor 50 million years ago. Even though they both rely on inherited mechanisms to specify their germ line, the integration of stage-matched scRNA seq datasets from these two sea urchins revealed, amongst others, a broader expression of Nanos2 in Lytechinus variegatus (Lv) compared to Strongylocentrotus purpuratus (Sp). more...

Organism:

Lytechinus variegatus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32500

12 Samples

Download data: MTX, RDS, TSV