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Items: 1 to 20 of 2006

1.

Structural and molecular distinctions of secondary and primary spines in the sea urchin Lytechinus variegatus

(Submitter supplied) Sea urchins (echinoids) are common model organisms for research in developmental biology and for their transition from a bilateral larva into their post-metamorphic adult with pentaradial body symmetry. The adult also has a calcareous endoskeleton with a multimetameric pattern of continuously added elements, among them the namesake of this phylum, spines. Nearly all echinoids have both large primary spines, and an associated set of smaller secondary spines.We hypothesize that the secondary spines of the tropical variegated urchin species, Lytechinus variegatus, are morphologically and molecularly distinct structures from primary spines and not just small spines. more...
Organism:
Lytechinus variegatus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL30656
8 Samples
Download data: TXT
Series
Accession:
GSE267428
ID:
200267428
2.

The brittle star genome illuminates the genetic basis of animal appendage regeneration

(Submitter supplied) Species within nearly all extant animal lineages are capable of regenerating body parts. However, it remains unclear whether the gene expression programme controlling regeneration is evolutionarily conserved. Brittle stars are a species-rich class of echinoderms with outstanding regenerative abilities, but investigations into the genetic bases of regeneration in this group have been hindered by the limited available genomic resources. more...
Organism:
Amphiura filiformis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL33902
28 Samples
Download data: TSV
Series
Accession:
GSE246675
ID:
200246675
3.

Pol II pausing is a milestone on the road to complex animals

(Submitter supplied) PRO-seq experiments in multiple organisms. Also, PRO-seq experiment of Nelfb and Nelfe degron mESC in serum/LIF with or without dTAG-13. 
Organism:
Escherichia coli; Mus musculus; Perkinsus marinus; Daphnia pulex; Strongylocentrotus purpuratus; Sphaeroforma arctica; Haloferax mediterranei; Dryas iulia; Nematostella vectensis; Dictyostelium discoideum; Capsaspora owczarzaki; Creolimax fragrantissima
Type:
Other
12 related Platforms
46 Samples
Download data
Series
Accession:
GSE223913
ID:
200223913
4.

Analysis of differentially expressed genes in the sea cucumber Apostichopus japonicus under heat stress

(Submitter supplied) The high-throughput RNA-seq was applied under both 26°C and 30°C heat stress in Apostichopus japonicus, which revealed characterization of gene expression at sub-lethal and lethal limit temperature. The results will help to better understand the characteristics of heat shock response in A. japonicus.
Organism:
Apostichopus japonicus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL32343
12 Samples
Download data: TXT
Series
Accession:
GSE205975
ID:
200205975
5.

Conservation and contrast in cell states of echinoderm ovaries

(Submitter supplied) In contrast to women, echinoderms have the amazing ability to keep producing functional gametes throughout their lifespan, in some cases exceeding 200 years. The histology and ultrastructure of echinoderm ovaries has been described but how these ovaries function and maintain the production of high-quality gametes is still a mystery. Here, we present the first single cell RNA sequencing (scRNAseq) datasets of two sea urchin species (Strongylocentrotus purpuratus and Lytechinus variegatus) and one sea star species (Patiria miniata). more...
Organism:
Lytechinus variegatus; Strongylocentrotus purpuratus; Patiria miniata
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL32500 GPL33874 GPL28450
3 Samples
Download data: MTX, RDS, TSV
Series
Accession:
GSE246430
ID:
200246430
6.

Molecular characterization of the sea urchin larva photosensory system: Insights into the evolution of a Go-Opsin positive neuronal population

(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
Series
Accession:
GSE240882
ID:
200240882
7.

Single-cell RNA sequencing of the Strongylocentrotus purpuratus larva reveals the blueprint of major cell types and nervous system of a non-chordate deuterostome

(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
Series
Accession:
GSE241045
ID:
200241045
8.

single nucleus RNA-seq of early development in P. miniata and S. purpuratus

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Strongylocentrotus purpuratus; Patiria miniata
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL33652 GPL29871
7 Samples
Download data: MTX, TSV
Series
Accession:
GSE240146
ID:
200240146
9.

single nucleus RNA-seq of early development S. purpuratus

(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
Series
Accession:
GSE240144
ID:
200240144
10.

single nucleus RNA-seq of early development in P. miniata

(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
Series
Accession:
GSE240143
ID:
200240143
11.

Widespread priming of transcriptional regulatory elements by incipient accessibility or Pol II pause in early embryos of the sea urchin Strongylocentrotus purpuratus

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Strongylocentrotus purpuratus
Type:
Genome binding/occupancy profiling by high throughput sequencing; Other; Third-party reanalysis
Platforms:
GPL20965 GPL23218
32 Samples
Download data: BW, NARROWPEAK
Series
Accession:
GSE234143
ID:
200234143
12.

Accessibility and activity of transcriptional regulatory elements during sea urchin embryogenesis and differentiation [PRO-seq]

(Submitter supplied) Transcriptional regulatory elements (TREs) are the primary nodes of the gene regulatory networks that control development. TREs are identified by PRO-seq and their accessibility by ATAC-seq during sea urchin embryonic development and differentiation. Our analysis identifies surprisingly early accessibility in 4-cell cleavage embryo TREs that is not necessarily followed by subsequent transcription, and an excess of ATAC-seq peaks transcriptionally disengaged during the stages analyzed. more...
Organism:
Strongylocentrotus purpuratus
Type:
Other; Third-party reanalysis
Platforms:
GPL20965 GPL23218
17 Samples
Download data: BED, BW
Series
Accession:
GSE234140
ID:
200234140
13.

Accessibility and activity of transcriptional regulatory elements during sea urchin embryogenesis and differentiation [ATAC-seq]

(Submitter supplied) Transcriptional regulatory elements (TREs) are the primary nodes of the gene regulatory networks that control development. TREs are identified by PRO-seq and their accessibility by ATAC-seq during sea urchin embryonic development and differentiation. Our analysis identifies surprisingly early accessibility in 4-cell cleavage embryo TREs that is not necessarily followed by subsequent transcription, and an excess of ATAC-seq peaks transcriptionally disengaged during the stages analyzed. more...
Organism:
Strongylocentrotus purpuratus
Type:
Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis
Platforms:
GPL23218 GPL20965
15 Samples
Download data: BED, BW, NARROWPEAK
Series
Accession:
GSE234139
ID:
200234139
14.

Comparative genomics of the sea urchin P. lividus highlights contrasting trends of genome and regulatory evolution in deuterostomes

(Submitter supplied) Sea urchins are emblematic marine animals with a rich fossil record and represent instrumental models for developmental biology. As echinoderms, sea urchins display several characteristics that set them apart from other deuterostomes such as their highly regulative embryonic development and their unique pentaradial adult body plan. To determine whether these characteristics are linked to particular genomic rearrangement or gene regulatory rewiring, we introduce a chromosome-scale genome assembly for sea urchin Paracentrotus lividus as well as extensive transcriptomic and epigenetic profiling during its embryonic development. more...
Organism:
Paracentrotus lividus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL32225
54 Samples
Download data: BW, TXT
Series
Accession:
GSE202034
ID:
200202034
15.

Elements of divergence in germline determination in closely related sea urchin species

(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
Series
Accession:
GSE208709
ID:
200208709
16.

Distinct mechanisms of germ cell factor regulation for an inductive germ cell fate

(Submitter supplied) Here we employed single cell RNA sequencing to identify the transcriptional program of Nanos and Vasa positive cells and their changes during development. Our single cell sequencing analysis of six developmental stages in P. miniata revealed cell types derived from the three germ layers and expression of the germ cell genes Nanos and Vasa. We used these datasets to parse out 20 cell lineages of the embryo identified by this approach and to focus on the key transitions of germ cell gene expression and test their coexpression with key signaling components.
Organism:
Patiria miniata
Type:
Expression profiling by high throughput sequencing
Platform:
GPL33863
6 Samples
Download data: MTX, RDS, TSV
Series
Accession:
GSE196654
ID:
200196654
17.

ChIP-seq H3K9ac in sea cucumber

(Submitter supplied) We presented a genome-wide characterization for H3K9 acetylation (H3K9ac) binding regions in normal temperature and heat-stress conditions via ChIP-seq. The results revealed H3K9ac was an extensive epigenetic modulation in A. japonicus. We further identified differentially acetylated regions (DARs) under heat stress.
Organism:
Apostichopus japonicus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL30874
12 Samples
Download data: NARROWPEAK
Series
Accession:
GSE186066
ID:
200186066
18.

Transcriptomic evolution across bilaterian tissues

(Submitter supplied) We investigate tissue transcriptomic evolution across bilaterian animals by analyzing RNA-seq data from eight different tissues across twenty species.
Organism:
Blattella germanica; Strongylocentrotus purpuratus; Octopus bimaculoides; Strigamia maritima; Branchiostoma lanceolatum; Danio rerio; Tribolium castaneum; Aedes aegypti; Xenopus tropicalis; Cloeon dipterum; Bombyx mori; Drosophila melanogaster; Callorhinchus milii; Monodelphis domestica; Episyrphus balteatus
Type:
Expression profiling by high throughput sequencing
15 related Platforms
89 Samples
Download data: TSV
Series
Accession:
GSE205498
ID:
200205498
19.

Three dimensional sectioning and full length gene expression profiling of Patiria miniata

(Submitter supplied) The affinity of the echinoderm pentaradial body plan with that of the ancestral bilateral symmetry remains one of the biggest zoological puzzle. Here, we revisited this classical zoological problem using RNA tomography and HCR in situ hybridization in the sea star Patiria miniata.
Organism:
Patiria miniata
Type:
Expression profiling by high throughput sequencing
Platform:
GPL32720
46 Samples
Download data: FASTA, TXT
Series
Accession:
GSE214723
ID:
200214723
20.

Gene expression profile at single cell level of nervous system in sea cucumber.

(Submitter supplied) nervous system plays key roles in sea cucumber. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of diverse cells in the nervous system.
Organism:
Apostichopus japonicus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL32343
1 Sample
Download data: MTX, TSV
Series
Accession:
GSE214016
ID:
200214016
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