Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1001850 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Recirculating juvenile seabass aquaculture Targeted loci environmental
| PRJNA513031 | ENA
Project description:In this study, we attempt to characterize the transcriptomic profile of the Asian seabass brains collected from the male and female sexes. The objective is to identify genes that show sexually dimorphic expression in the brain of this species. For this experiment, Asian seabass were collected from the Marine Aquaculture Center of the Agri-Food & Veterinary Authority of Singapore. There were no treatments carried out in this experiment. Four brains from adult male seabass (5 years old) with M3-type testis and four brains from adult female seabass (5 years old) with F3-type ovaries were used in this experiment. (Gonads were examined by histology and classified according to sexual maturation status as described by Guiguen and colleagues (Guiguen et al. Environmental Biology of Fishes, 1994)).
2015-01-08 | GSE53901 | GEO
Project description:To investigate the intestinal ileum response to dietary tryptophan deficiency and the contribution of the intestinal microbiome in regulating these responses
2023-02-21 | GSE222818 | GEO
Project description:In this study, we attempt to characterize the transcriptomic profile of the Asian seabass brains collected from the male and female sexes. The objective is to identify genes that show sexually dimorphic expression in the brain of this species. For this experiment, Asian seabass were collected from the Marine Aquaculture Center of the Agri-Food & Veterinary Authority of Singapore. There were no treatments carried out in this experiment. Four brains from adult male seabass (5 years old) with M3-type testis and four brains from adult female seabass (5 years old) with F3-type ovaries were used in this experiment. (Gonads were examined by histology and classified according to sexual maturation status as described by Guiguen and colleagues (Guiguen et al. Environmental Biology of Fishes, 1994)). Total 8 samples. Male Brain : 4 Female Brain : 4
2015-01-08 | E-GEOD-53901 | biostudies-arrayexpress
Project description:We compare the epigenomes of mouse intestinal epithelial cells at different intestinal regions and life stages of the mouse. We use a sequencing assay for transposase accessible chromatin (ATAC-seq) to determine highly accessible genomic regions. We determine regions that are differentially accessible between intestinal regions (duodenal crypt, duodenal villus, and colon) and between life stages (12-to-15-day-old/juvenile, 90-day-old/adult, and 21-month-old/geriatric).
2022-07-08 | GSE134579 | GEO
Project description:On going efforts are directed at understanding the mutualism between the gut microbiota and the host in breast-fed versus formula-fed infants. Due to the lack of tissue biopsies, no investigators have performed a global transcriptional (gene expression) analysis of the developing human intestine in healthy infants. As a result, the crosstalk between the microbiome and the host transcriptome in the developing mucosal-commensal environment has not been determined. In this study, we examined the host intestinal mRNA gene expression and microbial DNA profiles in full term 3 month-old infants exclusively formula fed (FF) (n=6) or breast fed (BF) (n=6) from birth to 3 months. Host mRNA microarray measurements were performed using isolated intact sloughed epithelial cells in stool samples collected at 3 months. Microbial composition from the same stool samples was assessed by metagenomic pyrosequencing. Both the host mRNA expression and bacterial microbiome phylogenetic profiles provided strong feature sets that clearly classified the two groups of babies (FF and BF). To determine the relationship between host epithelial cell gene expression and the bacterial colony profiles, the host transcriptome and functionally profiled microbiome data were analyzed in a multivariate manner. From a functional perspective, analysis of the gut microbiota's metagenome revealed that characteristics associated with virulence differed between the FF and BF babies. Using canonical correlation analysis, evidence of multivariate structure relating eleven host immunity / mucosal defense-related genes and microbiome virulence characteristics was observed. These results, for the first time, provide insight into the integrated responses of the host and microbiome to dietary substrates in the early neonatal period. Our data suggest that systems biology and computational modeling approaches that integrate “-omic” information from the host and the microbiome can identify important mechanistic pathways of intestinal development affecting the gut microbiome in the first few months of life. KEYWORDS: infant, breast-feeding, infant formula, exfoliated cells, transcriptome, metagenome, multivariate analysis, canonical correlation analysis 12 samples, 2 groups
2012-03-19 | E-GEOD-31075 | biostudies-arrayexpress
Project description:A human gut-on-a-chip microdevice was used to coculture multiple commensal microbes in contact with living human intestinal epithelial cells for more than a week in vitro and to analyze how gut microbiome, inflammatory cells, and peristalsis-associated mechanical deformations independently contribute to intestinal bacterial overgrowth and inflammation. This in vitro model replicated results from past animal and human studies, including demonstration that probiotic and antibiotic therapies can suppress villus injury induced by pathogenic bacteria. By ceasing peristalsis-like motions while maintaining luminal flow, lack of epithelial deformation was shown to trigger bacterial overgrowth similar to that observed in patients with ileus and inflammatory bowel disease. Analysis of intestinal inflammation on-chip revealed that immune cells and lipopolysaccharide endotoxin together stimulate epithelial cells to produce four proinflammatory cytokines (IL-8, IL-6, IL-1β, and TNF-α) that are necessary and sufficient to induce villus injury and compromise intestinal barrier function. Thus, this human gut-on-a-chip can be used to analyze contributions of microbiome to intestinal pathophysiology and dissect disease mechanisms in a controlled manner that is not possible using existing in vitro systems or animal models. 6 samples, 2 biological replicates for each 3 conditions.
2015-12-16 | E-GEOD-65790 | biostudies-arrayexpress