Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1291971 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Omics approaches are broadly used to explore endocrine and toxicity-related pathways and functions. Nevertheless, there is still a significant gap in knowledge in terms of understanding the endocrine system and its numerous connections and intricate feedback loops, especially in non-model organisms. The fathead minnow (Pimephales promelas) is a widely used small fish model for aquatic toxicology and regulatory testing, particularly in North America. A draft genome has been published but the amount of available genomic or transcriptomic information is still far behind that of other more broadly studied species, such as the zebrafish. Here, we surveyed the tissue-specific proteome and transcriptome profiles in adult male fathead minnow. To do so, we generated a draft transcriptome using short and long sequencing reads. We also performed RNA sequencing and proteomics analysis on the telencephalon, hypothalamus, liver, and gut of male fish. The main purpose of this analysis was to generate tissue-specific omics data in order to support future aquatic ecotoxicogenomic and endocrine-related studies as well as to improve our understanding of the fathead minnow as an ecological model.
2018-10-15 | PXD010216 | Pride
Project description:[original title] Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. We demonstrate extensive quantitative changes in binding of six factors that control early embryonic patterning between two closely related Drosophila species ChIP-Seq based binding measurements of six transcription factors in embryos of two Drosophila species, D.melanogaster and D.yakuba.
2010-02-18 | E-GEOD-20369 | biostudies-arrayexpress
Project description:This study examines genomic copy-number variation between two African cichlid species through array comparative genomic hybridization. Probe level hybridization ratios were compared to copy number variation identified in Illumina and Pacific Biosciences genome assemblies from both species. Array comparative genomic hybridization was performed with 3 samples (1 replicate array setup) of genomic DNA from Maylandia zebra vs. Orechromis niloticus XX clone genomic DNA from University of Stirling clonal lines.
2019-12-14 | GSE141976 | GEO
Project description:Array-based cross-species hybridization between genera of Rhabditidae (Nematoda)
| PRJNA130825 | ENA
Project description:Multifunctional TFs are central in coordinating development and metabolism in filamentous fungi. In this study, we systematically dissect the regulatory functions of NsdD, a highly conserved GATA-type TF in Pezizomycotina, using network-based multi-omics approaches in two distantly related species, A. nidulans and A. flavus. Our analyses reveal that NsdD governs fungal development and metabolism through species-specific GRNs, directly targeting key upstream regulators and genes involved in core cellular processes. These regulatory distinctions underlie the morphological and metabolic differences observed between the two species. Notably, our cross-species comparison uncovers extensive GRN rewiring, demonstrating how evolutionary divergence can reshape transcriptional networks even under conserved regulatory control. The resulting GRN maps offer a valuable framework for understanding gene regulation in Aspergillus and provide a foundation for broader studies on the evolution of transcriptional networks and conserved regulatory factors in filamentous fungi.
2025-05-29 | GSE219137 | GEO
Project description:Multifunctional TFs are central in coordinating development and metabolism in filamentous fungi. In this study, we systematically dissect the regulatory functions of NsdD, a highly conserved GATA-type TF in Pezizomycotina, using network-based multi-omics approaches in two distantly related species, A. nidulans and A. flavus. Our analyses reveal that NsdD governs fungal development and metabolism through species-specific GRNs, directly targeting key upstream regulators and genes involved in core cellular processes. These regulatory distinctions underlie the morphological and metabolic differences observed between the two species. Notably, our cross-species comparison uncovers extensive GRN rewiring, demonstrating how evolutionary divergence can reshape transcriptional networks even under conserved regulatory control. The resulting GRN maps offer a valuable framework for understanding gene regulation in Aspergillus and provide a foundation for broader studies on the evolution of transcriptional networks and conserved regulatory factors in filamentous fungi.
2025-05-29 | GSE219139 | GEO
Project description:We created a multi-species microarray platform, containing probes to the whole genomes of seven different Saccharomyces species, with very dense coverage (one probe every ~500 bp) of the S. cerevisiae genome, including non-S288c regions, mitochondrial and 2 micron circle genomes, plus probes at fairly dense coverage (one probe every ~2,100 bp) for each of the genomes of six other Saccharomyces species: S. paradoxus, S. mikatae, S. kudriavzevii, S. bayanus, S. kluyveri and S. castellii. We performed array-Comparative Genomic Hybridization (aCGH) using this platform, examining 83 different Saccharomyces strains collected across a wide range of habitats; of these, 69 were widely used commercial S. cerevisiae wine strains, while the remaining 14 were from a wide range of other industrial and natural habitats. Thus, we were able to sample much of the pan-genome space of the Saccharomyces genus. We observed interspecific hybridization events, introgression events, and pervasive copy number variation (CNV) in all but a few of the strains. These CNVs were distributed throughout the strains such that they did not produce any clear phylogeny, suggesting extensive mating in both industrial and wild strains. To validate our results and to determine whether apparently similar introgressions and CNVs were identical by descent or recurrent, we also performed whole genome sequencing on nine of these strains. These data may help pinpoint genomic regions involved in adaptation to different industrial milieus, as well as shed light on the course of domestication of S. cerevisiae.
2012-02-01 | GSE26689 | GEO
Project description:[original title] Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. We demonstrate extensive quantitative changes in binding of six factors that control early embryonic patterning between two closely related Drosophila species
2010-02-18 | GSE20369 | GEO