Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1238495 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR32786301.fastq.gz | Fastqsanger.gz | |||
| SRR32786301_1.fastq.gz | Fastqsanger.gz | |||
| SRR32786301_2.fastq.gz | Fastqsanger.gz | |||
| SRR32786302.fastq.gz | Fastqsanger.gz | |||
| SRR32786302_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 93 |
Similar Datasets
Project description:Individual male broilers (Cobb500; n=16) were allotted to 4 experimental diets containing either no phytogenic feed additives, an essential oil blend, saponin extract or a combination of both phytogenic preparations. Liver samples were used for transcriptome profiling.
2017-12-31 | GSE95566 | GEO
Project description:Individual male broilers (Cobb500; n=16) were allotted to 4 experimental diets containing either no phytogenic feed additives, an essential oil blend, saponin extract or a combination of both phytogenic preparations. Jejunum samples were used for transcriptome profiling.
2017-12-31 | GSE95559 | GEO
Project description:The TET-family enzymes (TETs) convert methylcytosine to hydroxymethylcytosine, a lately discovered epigenetic modification that can modulate transcription. While recent reports suggest that TETs may play a role in response to oxidative stress, this role remains uncertain. Here we show that Tet1 is sensitive to peroxide and report a global decrease in hydroxymethylcytosine in cells treated with BSO and in the intestinal epithelium of mice lacking the major antioxidant enzymes glutathione peroxidases 1 and 2. Furthermore, genome-wide profiling revealed differentially hydroxymethylated regions in genes involved in responses to oxidative stress. Intriguingly, a considerable proportion of these regions lie in genes encoding microRNAs predicted to target transcripts involved in oxidative stress response. This work thus demonstrates a profound effect of oxidative stress on the hydroxymethylome and opens exciting new avenues of research by highlighting a set of microRNAs that may participate in the prevention or etiology of oxidative-stress-related diseases. Examination of DNA hydroxymethylation landscape in SY5Y cell lines and in intestinal epithelium of mice.
2016-01-14 | E-GEOD-59718 | biostudies-arrayexpress
Project description:<p>Immune stress in broilers can cause severe economic losses, chlorogenic acid is an effective plant extract for alleviating immune stress. This study investigates the effect of chlorogenic acid on the intestinal microbiota and metabolites of broilers under immune stress. 312 broilers were randomly divided into 4 treatment groups, namely saline group, lipopolysaccharides (LPS) group, saline+chlorogenic acid (SCGA) group, and LPS+CGA (LCGA) group. The LPS group and LCGA group of broilers were injected with 0.5 mg/kg LPS intraperitoneally at 14, 15, and 17 days of age to induce immune stress. SCGA and LCGA group fed a basal diet supplemented with 1000 mg/kg CGA. At 17d, the ileal contents of broilers were collected for microbial and metabolomics analysis. Results showed that immune stress led Subdoligranulum decreased, thereby lowering the diversity of the intestinal microbial community. CGA increase the abundance of beneficial bacteria Clostridiaceae and Candidatus Arthromitus in the ileum of immune-stressed broilers, while reducing the abundance of Lachnospiraceae, Allobaculum, Desulfovibrio, Desulfovibrionales, Desulfovibrionaceae. Non-targeted metabolomics results showed that immune stress significantly increased the content of methylmalonic acid, N-Acetyl-L-aspartic acid, trans-ferulic acid, and pantothenic acid in the ileum of broilers, while significantly downregulated the content of pyroglutamic acid, L-glutamic gamma-semialdehyde, and biliverdin, indicating that LPS activated inflammation and oxidation in broilers, leading to oxidative damage in the intestine. After CGA added, the levels of corticosterone, prostaglandin B2, trans-ferulic acid, methylmalonic acid in the ileum of immune-stressed broilers were significantly lower, while the levels of pyroglutamic acid, L-glutamic gamma-semialdehyde, biliverdin, chenodeoxycholic acid, desmosterol, and 4-hydroxycinnamic acid were significantly higher, indicating that CGA can alleviate the inflammatory response induced by immune stress and enhance antioxidant capacity. Therefore, CGA can alleviate immune stress by regulating the ileal microbiota and metabolites.</p>
2025-06-09 | MTBLS11790 | MetaboLights
Project description:The intestinal microbiome forms dynamic ecosystem whose balanced composition and functioning are essential for maintaining overall gut health and well-being in living organisms. In broilers, dysbiosis disrupts the microbiota-host balance, often without obvious clinical symptoms but with intestinal inflammation, leading to impaired animal performance and significant economic losses. This study utilizes an in vivo model of dysbiosis to investigate the blood proteome response of broilers to intestinal imbalance. Microscopic histological changes in the gut (shorter villi, increased crypt depth, p<0.0001) were observed in the duodenal and jejunal tissue of challenged birds. Elevated levels of permeability markers faecal ovotransferrin (p < 0.0001) and serum iohexol (p= 0.0009) additionally indicated increased intestinal permeability in challenged group compared to control. The MS/MS-based proteomics analysis was performed on broilers’ blood plasma enabling identification of 388 proteins, 25 of which demonstrated significant difference between the groups. Functional analysis showed activation of immune response, signalling, and interspecies interaction, while proteins related to cellular physiology, cell-cell communication, and extracellular matrix (ECM) processes were suppressed. Protein-protein interaction (PPI) analysis revealed two clusters of downregulated proteins involved in ECM organization and cell adhesion. These results suggest that the dysbiosis challenge alters plasma protein expression as the host prioritizes immune defense over structural maintenance. The activation of immune processes and suppression of ECM pathways highlight potential biomarkers and therapeutic targets for addressing dysbiosis.
2025-07-14 | PXD056546 | Pride
Project description:Long chain sulfated polysaccharides such as fucoidans are promising feed additives to improve animal health and welfare. Thus, our study evaluated the bioactive properties of a fucoidan-enriched fraction from sugar kelp (Saccharina lattissima) on the intestinal transcriptome of pre-smolts Atlantic salmon (Salmo salar) fed with novel functional aquafeeds for 5 weeks in freshwater.
2025-09-12 | GSE297881 | GEO
Project description:Detergents and salts are widely used in lysis buffer to enhance protein extraction from biological samples, facilitating in-depth proteome analysis, however, to efficiently remove these detergent and salt additives from the digested peptides is essential for generating high quality mass spectra in LC-MS/MS analysis. The sample preparation methods, such as Filter-Aided Sample Preparation (FASP), acetone precipitation followed by in-solution digestion (AP), strong cation exchange-based centrifugal proteomic reactor (CPR), are commonly used for proteomic sample process, but the additives removal efficiency and the application scope of these methods need to be further investigated. In this study, we demonstrated an integrative work flow for systematical small molecular additives quantification as well as peptide/protein identification to provide a comprehensive evaluation for additive cleanup effect of proteomic sample preparation pipelines. The multiple reaction monitoring (MRM)-based LC-MS approach was developed for six additives (i.e., Tris, Urea, CHAPS, SDS, SDC and Triton X-100) quantification. For the peptide and protein identification, although FASP outperformed the other two methods, these three methods were complementary to each other, in terms of peptide/ protein identification, as well as GRAVY index and amino acids distributions. By integrating analysis of small molecular quantification and protein identification datasets, we first bridged the quantitative influence of additive concentration to the peptide analysis performance. Our results provide a valuable dataset for appropriate sample preparation method selection and a guideline for evaluation of small molecular additives cleanup efficiency in the sample preparation procedures.
2017-08-11 | PXD005405 | Pride
Project description:Oxidative stress and celllular apoptosis of intestinal epithelial tissues relies on the environments from drinking different waters. In the rat intestinal epithelium, the toxic materials or antioxidant materials may affect the genes expression of oxidative stress and apoptosis through the oral intake ofa waters or agents. The up- or down-regulation in the antioxidant genes and apoptosis-related genes may represent the internal microenvironments in the intestine. Therefore, we used intestinal epithelium from rats drinking different waters to test the several genes expression. We used microarrays to detail the global programme of gene expression underlying damage or protection effect and identified distinct classes of up-regulated or down-regulated genes during drinking different waters test in this process.
2014-12-01 | GSE55142 | GEO
Project description:Feed additives aiming to improve gastrointestinal health are frequently supplied to piglets after weaning but might be more effective when administered before weaning. In this period, feed additives can either be administered directly to neonates, or indirectly via sow’s feed. It is yet unknown what the effect of the administration route is on gut functionality and health. Therefore, we compared the effect of different dietary interventions on gut functionality after maternal administration (lactation feed) to the neonatal administration route (oral gavage). These feed interventions included medium chain fatty acids (MCFA), beta-glucans (BG), and galacto-oligosaccharides (GOS). We measured intestinal gene expression and microbiota composition after birth (d1) and after weaning (d31). Our results show that the type of intervention and the administration route influence gut functionality (microbiome and gene expression profiles). MCFA administration led to a more differentially orchestrated response when comparing the neonatal and maternal administration route then the other two additives, indicating the route of administration of the feed interventions is determinative for the outcome. This implies that for each nutritional intervention in early life of a pig the optimal route of administration needs to be determined.
2023-06-01 | GSE229947 | GEO