Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1037283 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Colonization of carbonate rocks by groundwater bacteria
| PRJNA1005956 | ENA
Project description:Organisms adapt to and survive in environments with varying nutrient availability. Cis-regulatory changes play important roles in adaptation and phenotypic evolution. To what extent cis-regulatory elements contribute to metabolic adaptation is less understood. Here we have utilized a unique vertebrate model, Astyanax mexicanus, that survives in nutrient rich surface and nutrient deprived cave water to uncover gene regulatory networks in metabolic adaptation. We performed genome-wide analysis of accessible chromatin and histone modifications in the liver tissue of one surface and two independently derived cave populations, providing the first genome-wide epigenetic landscape in this organism. We find that many cis-regulatory elements differ between surface and the cavefish, while the two independently derived cave populations have evolved remarkably similar regulatory signatures. Changes in gene regulatory networks between the surface and cave morphotypes point to global changes in key metabolic pathways.
2021-09-07 | GSE153049 | GEO
Project description:Organisms adapt to and survive in environments with varying nutrient availability. Cis-regulatory changes play important roles in adaptation and phenotypic evolution. To what extent cis-regulatory elements contribute to metabolic adaptation is less understood. Here we have utilized a unique vertebrate model, Astyanax mexicanus, that survives in nutrient rich surface and nutrient deprived cave water to uncover gene regulatory networks in metabolic adaptation. We performed genome-wide analysis of accessible chromatin and histone modifications in the liver tissue of one surface and two independently derived cave populations, providing the first genome-wide epigenetic landscape in this organism. We find that many cis-regulatory elements differ between surface and the cavefish, while the two independently derived cave populations have evolved remarkably similar regulatory signatures. Changes in gene regulatory networks between the surface and cave morphotypes point to global changes in key metabolic pathways.
2021-09-07 | GSE153048 | GEO
Project description:we report a transcriptome-wide comparative investigation between surface and cave species in Sinocyclocheilus. De novo transcriptome assemblies were performed on surface and cave species; then the Sinocyclocheilus contigs were annotated with Gene Ontology. RNA-Seq assays revealed reduced transcription of a series of visual phototransduction and retinal disease related genes in cave-dwelling species compared with surface species. Degeneration of the retina in Sinocyclocheilus cavefish might occur in a lens-independent way by the down-regulation of several transcriptional factors, which have direct roles in retina development and maintenance, such as crx, rorb and Wnt pathway members. Examination of 2 different eye samples in 2 Sinocyclocheilus species.
2013-03-31 | E-GEOD-40446 | biostudies-arrayexpress
Project description:Amorphous calcium carbonate (ACC) is a non-crystalline form of calcium carbonate, which is composed of aggregated nano-size primary particles. Here, we wanted to evaluate how ACC affects gene expression in a human lung cancer cell line (A549).
2023-08-21 | GSE235316 | GEO
Project description:Alkalinity stress is considered to be one of the major stressors for fish in saline-alkali water. Thus, it is of great significance from both aquaculture and physiological viewpoint to understand the molecular genetic response of aquatic organisms to alkalinity stress. The objective of this study is to determine genome-wide gene expression profiles to better understand the physiology response of medaka (Oryzias latipes) to high carbonate alkalinity stress. In lab-based cultures, adult fish were exposed to freshwater and high carbonate alkalinity water .We designed a microarray containing 26429 oligonucleotides and describe our experimental results for measuring gene expression changes in the gill of carbonate alkalinity stress exposed fish. The fish were exposed to freshwater (FW) and high carbonate alkalinity water (AW) for 96h, each with three replicates.
2014-01-24 | E-GEOD-27298 | biostudies-arrayexpress
Project description:we report a transcriptome-wide comparative investigation between surface and cave species in Sinocyclocheilus. De novo transcriptome assemblies were performed on surface and cave species; then the Sinocyclocheilus contigs were annotated with Gene Ontology. RNA-Seq assays revealed reduced transcription of a series of visual phototransduction and retinal disease related genes in cave-dwelling species compared with surface species. Degeneration of the retina in Sinocyclocheilus cavefish might occur in a lens-independent way by the down-regulation of several transcriptional factors, which have direct roles in retina development and maintenance, such as crx, rorb and Wnt pathway members.
2013-03-31 | GSE40446 | GEO