Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1101037 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR28707000_1.fastq.gz | Fastqsanger.gz | |||
| SRR28707000_2.fastq.gz | Fastqsanger.gz | |||
| SRR28707001_1.fastq.gz | Fastqsanger.gz | |||
| SRR28707001_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 145 |
Similar Datasets
Project description:Rainbow trout (Oncorhynchus mykiss) were fed during 4 weeks with either a control diet or an immunostimulant diet and then injected with LPS to investigate the effect of dietary immunostimulation in the portals of entry, intestine and gills, using a salmonid-specific microarray platform enriched with immune-related genes. IS-diet feeding significantly changed transcriptomic expression profiles in response to LPS: significant changes in genes and functional GO categories related to remodeling processes and antigen presentation were different for both diets. The results revealed that one of the main effects of IS-diets in trout is the increase of genes involved in antigen recognition and in adaptive immunity. Keywords: gills, intestine, immunostimulats, transcriptomic response, trout
2008-10-02 | GSE12961 | GEO
Project description:The objective of this study was to identify metabolic regulatory mechanisms affected by choline availability in rainbow trout (Oncorhynchus mykiss) broodstock diets associated with increased offspring growth performance. Three customized diets were formulated to have different levels of choline: (a) 0% choline supplementation (Low Choline: 2065 ppm choline), (b) 0.6% choline supplementation (Medium Choline: 5657 ppm choline), and (c) 1.2% choline supplementation (High Choline: 9248 ppm choline). Six all-female rainbow trout families were fed experimental diets beginning 18 months post-hatch until spawning; their offspring were fed a commercial diet. Experimental broodstock diet did not affect overall choline, fatty acid, or amino acid content in the oocytes (p > 0.05), apart from tyrosine (p ≤ 0.05). Offspring body weights from the High and Low Choline diets did not differ from those in the Medium Choline diet (p > 0.05); however, family-by-diet and sire-by-diet interactions on offspring growth were detected (p ≤ 0.05). The High Choline diet did not improve growth performance in the six broodstock families at final harvest (520-days post-hatch, or dph). Numerous genes associated with muscle development and lipid metabolism were identified, including myosin, troponin C, and fatty acid binding proteins, which were associated with key signaling pathways of lipid metabolism, muscle cell development, muscle cell proliferation, and muscle cell differentiation. These findings indicate that supplementing broodstock diets with choline does regulate expression of genes related to growth and nutrient partitioning but does not lead to growth benefits in rainbow trout families selected for disease resistance.
2024-02-09 | GSE243186 | GEO
Project description:The sustainable growth of fish aquaculture will require the procurement of non-marine feed sources. Glycerol is a potential feed supplement whose metabolism may spare the catabolism of dietary amino acids, thereby extending the use of the feed protein to other physiological functions such as growth. In the present study, the effects of dietary glycerol supplementation on the muscle and liver metabolomes of rainbow trout (Oncorhynchus mykiss) and European seabass (Dicentrarchus labrax) were evaluated. Fish juveniles were fed diets with 0%, 2.5%, and 5% glycerol. Muscle and liver aqueous fractions were extracted and 1H NMR spectra were acquired. Metabolite profiles derived from the 1H NMR signals were assessed using univariate and multivariate statistical analyses. The adenylate energy charge was determined in the muscle. For both species, the muscle metabolite profile showed more variability compared to that of the liver and was most perturbed by the 5.0% glycerol diet. For the liver metabolite profile, rainbow trout showed fewer differences compared to European seabass. No differences were observed in energy charge between experimental groups for either species. Thus, rainbow trout appeared to be less susceptible to tissue metabolite perturbations, compared to seabass, when the diet was supplemented with up to 5% glycerol.
2020-02-24 | MTBLS832 | MetaboLights
Project description:We used fish from two divergent lines of rainbow trout, selected for low or high muscle fat content (respectively L and F lines) and fed two different diets, containing either 10% (LE diet) or 23% (HE diet) lipids. For more details about experimental fish and diets, see Kolditz et al.,Am J Physiol Regul Integr Comp Physiol 294: R1154–R1164, 2008. There are 4 experimental conditions: L-LE, L-HE, F-LE and F-HE. This experiment contain the data derived from the hybridization of the RNA extracted from individual liver of these fish. for each membrane, spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array. Keywords: Nutritional genomics, response to divergent selection for muscle fattening, liver metabolism, rainbow trout
2008-09-01 | GSE12031 | GEO
Project description:The sustainable development of modern aquaculture must rely on a significant reduction of the fish meal (FM) used in aquafeed formulations. However, FM substitution with alternative ingredients in diets for carnivorous fish species often showed reduced nutrient absorption, significantly perturbed metabolisms and histological changes at both hepatic and intestinal level. In the present study, adult rainbow trout (Oncorhynchus mykiss) were fed three different experimental aquafeed formulations. A control diet with higher FM content (27.3%) than two test formulations in which fish meal was substituted with two more sustainable and promising alternatives: insect meal (Hermetia illucens larvae=10.1%, FM=11.6%) and poultry by-products meal (PBM=14.8%; FM=11.7%). Combined metabolomics and proteomics analyses of fish liver, together with histological examination of liver and intestine demonstrated that a well balanced formulation of nutrients in the three diets allowed high metabolic compatibility of either substitutions, paving the way for innovative and sustainable use of novel raw materials for the fish feed industry. Results show that the main metabolic pathways of nutrient absorption and catabolism were essentially unaltered by alternative feed ingredients, and also histological alterations were negligible. It is demonstrated that substitution of fish meal with sustainable alternatives does not impact on fish metabolism, given proper efforts are put in fulfilling nutritional requirements of rainbow trout.
2022-07-18 | PXD033201 | Pride
Project description:We used fish from two divergent lines of rainbow trout, selected for low or high muscle fat content (respectively L and F lines) and fed two different diets, containing either 10% (LE diet) or 23% (HE diet) lipids. For more details about experimental fish and diets, see Kolditz et al.,Am J Physiol Regul Integr Comp Physiol 294: R1154–R1164, 2008. There are 4 experimental conditions: L-LE, L-HE, F-LE and F-HE. This experiment contain the data derived from the hybridization of the RNA extracted from individual liver of these fish. for each membrane, spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array. Keywords: Nutritional genomics, response to divergent selection for muscle fattening, liver metabolism, rainbow trout 32 samples
2008-09-01 | E-GEOD-12031 | biostudies-arrayexpress
Project description:We investigate mechanisms behind the response to a plant based diet at short term, by analyzing the transcriptome of 3 isogenic lines of rainbow trout (R23, AB1, A22). These families represent an interesting genetic material to work on as they have similar responses when fed marine based-diet (M diet) but highly different responses when fed a plant-based diet (V diet). Transcriptomic analyses of whole fry revealed 1740, 1834 and 246 probes differentially expressed among the three isogenic lines. Gene ontology enrichment analysis revealed different enriched pathways. Among them, some were related to immunity and perception. Among ontologies related to metabolism only the methionine metabolism pathway was found to be significantly enriched. First, the use of these isogenic lines of rainbow trout led to find new pathways related to plant-based diets utilization which had not been described previously. Secondly, difference in expression of genes related to immunity suggest that this function play an important role but specific effect on immune status was difficult to assess, and further investigations are needed. Finally, results suggested that mechanisms underlying the use of plant-based diets is more linked to feed intake rather than to metabolism. Research on plants components affecting feed intake should be further explored to continue to improve feed formulation and reduce the reliance of aquaculture on marine resources without affecting fish performance.
2018-09-21 | GSE92673 | GEO
Project description:The objective of this paper was to determine whether shifts in the methylome in rainbow trout (Oncorhynchus mykiss) are correlated with transcriptomic changes during early development in response to maternal dietary choline intake. Three experimental diets were formulated to have different levels of choline: (a) 2065 ppm choline (Low Choline, 0% supplementation), (b) 5657 ppm choline (Medium Choline, 0.6% supplementation), and (c) 9248 ppm choline (High Choline, 1.2% choline supplementation). Six rainbow trout families were fed experimental diets beginning 18 months post-hatch until spawning; their offspring were fed a commercial diet. Reduced representational bisulfite sequencing (RRBS) was utilized to measure genome-wide methylation differences in offspring immediately after hatching. When comparing to the Medium Choline offspring, differential DNA methylation occurred more in the Low Choline offspring than High Choline, especially in genic features like promoters. The differentially methylated CpGs (q ≤ 0.01) were identified evenly between CpG islands and shores in the genome, mostly found in the introns of genes. Genes such as fabp2 and leap2B associated with protein binding, fatty acid binding, DNA binding, and response to bacteria were differentially methylated and detected as differentially regulated genes by previous RNA-seq analysis. Although these findings indicate that levels of dietary choline available in broodstock diets alters offspring DNA methylation; most differentially expressed genes were not associated with differential DNA methylation, suggesting additional mechanisms playing a role in regulating gene expression in response to maternal choline intake.
2024-11-21 | GSE269087 | GEO
Project description:Indole-3-carbinol (I3C) and 3,3’-diindolylmethane (DIM), a primary I3C derivative in vivo, are known dietary chemopreventive agents also available as dietary supplements. However, I3C has been found to act as a tumor promoter in rat (multi-organ) and trout (liver) models. I3C and DIM were previously found to be estrogenic in trout liver based on toxicogenomic profiles. In this study, we compare the post-initiation effects of DIM and 17β-estradiol (E2) on aflatoxin B1 (AFB1)-induced hepatocarcinogenesis in trout. Trout were initiated as embryos with 50 ppb AFB1, fed control diet for three months followed by diets containing 0, 120 or 400 ppm DIM or 5 ppm E2 for 18 weeks before returning all groups to control diet. Tumor incidence was determined 13 months later and found to be significantly elevated in AFB1-initiated trout fed either 400 ppm DIM or 5 ppm E2 compared to control animals. To evaluate the mechanism of tumor enhancement, hepatic gene expression profiles were examined in animals fed promotional diets during the course of tumorigenesis and in hepatocellular carcinomas (HCCs) of initiated animals using a rainbow trout 70-mer custom oligonucleotide array. We demonstrate that DIM alters gene expression profiles similar to E2 in liver samples during tumorigenesis and in HCC tumors. Further, HCCs from animals on DIM and E2 promotional diets had a transcriptional signature indicating decreased invasive or metastatic potential compared to HCCs from control animals. Overall, these findings are the first to demonstrate tumor promotion by DIM. They confirm the importance of estrogenic signaling in the mechanism of promotion by dietary indoles in trout liver and indicate a possible dual effect that enhances tumor incidence and decreases potential for metastasis. Keywords: time course
2006-12-31 | GSE5644 | GEO