Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR33618373_1.fastq.gz | Fastqsanger.gz | |||
| SRR33618373_2.fastq.gz | Fastqsanger.gz | |||
| SRR33618374_1.fastq.gz | Fastqsanger.gz | |||
| SRR33618374_2.fastq.gz | Fastqsanger.gz | |||
| SRR33618375_subreads.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 7 |
Similar Datasets
Project description: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 other echinoderms.
2019-07-10 | GSE131370 | GEO
Project description: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. Here, we report a chromosome-scale genome assembly for the brittle star Amphiura filiformis. We show that the brittle star displays the most rearranged genome amongst echinoderms sequenced to date, featuring a reorganised Hox cluster reminiscent of the rearrangements observed in sea urchins. In addition, we performed an extensive profiling of gene expression throughout brittle star adult arm regeneration and identified sequential waves of gene expression governing wound healing, proliferation and differentiation. We conducted comparative transcriptomic analyses with other invertebrate and vertebrate models for appendage regeneration and uncovered hundreds of genes with conserved expression dynamics, notably during the proliferative phase of regeneration. Our findings emphasise the crucial importance of echinoderms to detect long-range expression conservation between vertebrates and classical invertebrate regeneration model systems.
2024-05-07 | GSE246675 | GEO
Project description:Collagenous connective tissue is responsible for body integrity in all multicellular organisms and has many biomedical applications within a multibillion-dollar industry. An inspiration for a new generation of collagen-based biomaterials with a wide range of applications may come from echinoderms, a group of marine invertebrates that includes sea stars, sea cucumbers, brittle stars, sea urchins, and sea lilies. Echinoderms are capable of reversibly controlling the pliability of certain connective tissue components (i.e., tendons and ligaments) that are composed of mutable collagenous tissue (MCT). The MCTs variable tensility allows echinoderms to perform unique functions, including energy-saving posture maintenance, autotomy, and asexual reproduction. It is known that neurosecretory juxtaligamental cells in the nervous system control the MCT. These cells release substances that either soften or stiffen the MCT. So far, only a few of these substances have been purified and characterized, and the genomics behind MCT biology are still mostly unknown. Therefore, we propose to identify the putative MCT-related genes in echinoderms and better understand the biology of the juxtaligamental cells. Our research improves our knowledge about the MCT molecular control mechanism, with the ultimate goal of unlocking new biomaterial applications. In this project, we utilize RNA-Seq to identify and annotate differentially expressed genes in the MCT structures of the brittle star Ophiomastix wendtii
2024-12-13 | GSE278778 | GEO
Project description:Viral Communities within Echinoderms Metagenome
| PRJNA223197 | ENA
Project description: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). We find 14 cell states in the Sp ovary, 16 cell states in the Lv ovary and 13 cell states in the ovary of the sea star. This resource is essential to understand the structure and functional biology of the ovary in echinoderms, and better informs decisions in the utilization of in situ RNA hybridization probes selective for various cell types. We link key genes with cell clusters of the feature plots in validation of this approach. This resource also aids in the identification of the stem cells for prolonged and continuous gamete production, is a foundation for testing changes in the annual reproductive cycle, and is essential for understanding the evolution of reproduction of this important phylum. Highly selective gene expression revealed by this dataset also divulges gene targets of highest priority for interrogating gene activities by Cas9-targeted gene knock-out and knock-in approaches and in dissociated ovarian cell cultures to test the function of each cell type identified.
2023-11-29 | GSE246430 | GEO
Project description: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. To date, however, no genome-wide comparisons have been performed in order to provide an unbiased assessment of the evolution of GRNs between these taxa; and no study has attempted to determine the interplay between transcription factor binding motif evolution and GRN topology. The study here measures genome-wide binding of Tbrain orthologs using ChIP-seq, and associates these with putative target genes to assess global function. Targets of both factors are enriched for other regulatory genes, although non-overlapping sets of functional enrichments in the two datasets suggest a much diverged function. The number of low affinity binding motifs are significantly depressed in sea urchins compared to sea star, but both motifs types are associated with genes from a range of functional categories. Only a small fraction (~10%) of genes are predicted to be orthologous targets. Collectively these data indicate that Tbr has evolved significantly different developmental roles in these echinoderms, and that the maintained and unique targets, and their associated binding motifs are dispersed throughout the hierarchy of the GRN, rather than being biased towards terminal process or discrete functional blocks suggesting extensive evolutionary tinkering.
2016-12-01 | GSE89862 | GEO
Project description:Interventions: Genomic test CANCERPLEX-JP OncoGuide NCC oncopanel system FndationONe CDx genome profile GUARDANT360 MSI Analysis System BRACAnalysis
Primary outcome(s): Development of genome database
Study Design: Single arm Non-randomized
| 2643590 | ecrin-mdr-crc
Project description:Hox and ParaHox genes encode transcription factors with conserved similar expression patterns in divergent animals. The Pdx (Xlox) homeobox gene, for example, is expressed in a sharp spatial domain in the endodermal cell layer of the gut in chordates, echinoderms, annelids and molluscs. The significance of comparable gene expression patterns is unclear because it is not known if downstream transcriptional targets are also conserved. We thus conducted experiments to show that a classic transcriptional target of Pdx1 in vertebrates, the insulin gene, is also a direct target of Pdx in the Pacific oyster. We report that oyster has a diversity of insulin-related genes including one co-expressed with Pdx in the endodermal layer of oyster digestive tissue. Transcriptome analysis reveals functional similarity of this tissue to vertebrate pancreas. Using ATAC-seq we identify a Pdx homeodomain binding site upstream of the endodermally-expressed oyster insulin-related gene and using cell culture demonstrate that oyster Pdx acts as a transcriptional activator through this site. These data argue that a classic homeodomain-target gene interaction dates back to the base of Bilateria.
2021-03-28 | GSE107713 | GEO