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Strongylocentrotus purpuratus developmental transcriptomes
Transcriptomes of sea urchin (Strongylocentrotus purpuratus) embryos, larvae, and adult tissues were profiled using RNA-seq technology. -
The sea urchin larval response to immune challenge with Vibrio diazotrophicus
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... -
Genome-wide Targets of Ets1, Alx1 and MAPK pathway in Strongylocentrotus purp...
Total RNA was extracted at 28-30 hours post-fertilization (early gastrula stage) from Ets1 morphant embryos, Alx1 morphant embryos, embryos treated continuously with UO126 from... -
The evolution of DNA methylation inheritance and programming in animals
DNA methylation has been found throughout animal kingdom, but it is still unclear whether this epigenetic mechanism affects the evolution of genomic elements in animals. Here,... -
Chromatin accessibility profiling identifies cis-regulatory modules in an ear...
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... -
Genome-wide identification of binding sites and gene targets of Alx1, a pivot...
ChIP-seq provides a genome-wide view of the binding sites of Alx1, a pivotal transcription factor in a gene regulatory network that controls skeletogenesis in sea urchins and... -
DNA Zoo
The DNA Zoo is a consortium focused on facilitating conservation efforts through the rapid generation and release of high-quality genomics resources. -
PRO-seq, ATAC-seq, and Pol II ChIP-seq in 20 hour sea urchin embryos (ChIP-seq)
PRO-seq, ATAC-seq, and Pol II ChIP-seq signals are used to predict active developmental enhancers. Overall design: Machine learning models are trained and tested wit the... -
Accessibility and activity of transcriptional regulatory elements during sea ...
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... -
Base-resolution DNA hydroxymethylation maps of purple sea urchin (Strongyloce...
Using ACE-seq we investigated single-base resolution hydroxymethylomes of sea urchin, lancelet and zebrafish during development. Overall design: ACE-seq was perfomred on (i) 24... -
Regulation of dynamic pigment cell states at single-cell resolution
Pigment cells bear molecules with diverse physiological roles across phylogeny and are often under strict evolutionary selection. Thus, the mechanisms of regulating these cells,... -
An ancestral Wnt-Brachyury feedback loop and vertebrate-specific recruitment ...
Transcription factor brachyury plays a key role during mesoderm development in vertebrates. In this study we study study the effect of this transcription factor in diploblastic... -
Sea urchin sequencing data
Sea urchin sequencing data -
Transcriptomic evolution across bilaterian tissues
We investigate tissue transcriptomic evolution across bilaterian animals by analyzing RNA-seq data from eight different tissues across twenty species. Overall design:... -
Select microRNAs are essential for early development in the sea urchin.
microRNAs (miRNAs) are small noncoding RNAs that mediate post-transcriptional gene regulation and have emerged as essential regulators of many developmental events. The... -
Evolutionary recruitment of flexible Esrp-dependent splicing programs into di...
Epithelial-mesenchymal interactions are crucial for the development of multiple animal structures. Thus, unraveling how molecular tools are recruited in different lineages to... -
Strongylocentrotus purpuratus Raw sequence reads
4C-seq was performed to capture the chromatin regions that are in 3D proximity of Hox11/13 promoter from the developing embryos at 15 and 48 hours post fertilization. -
Conservation and diversity in genes that construct spines of the sea urchin
RNA sequencing of spines from four diverse sea urchin species (H.</p><p>pulcherrimus, E.tribuloides, Lytechinus variegatus, Strongylocentrotus purpuratus) to examine... -
GRIP-seq data for S. purpuratus, 24hpf embryos
This is the inaugural dataset for the new GRIP-seq method to map cis-regulatory regions genome-wide. This dataset is for the purple sea urchin embryo, S. purpuratus, at 24 hours... -
Purple sea urchin whole genome sequencing
Purple sea urchins are excellent model organisms for evo-devo research. Here, we sequence the whole genome of 140 purple sea urchins from 7 populations along the west coast of...
