Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1195667 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31644152_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR31644153_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR31644154_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR31644155_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR31644156_subreads.fastq.gz | Fastqsanger.gz |
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Project description:As an essential micronutrient for animals, vitamin E plays crucial physiological roles in reproduction, antioxidant and immune functions, and lipid metabolism. The objective of this study was to reveal molecular mechanism of vitamin E on intramuscular fat (IMF) deposition through transcriptome sequencing of pectoral muscle in broiler chickens. A total of 240 one-day-old health female chicks were randomly allocated into five dietary treatments with each treatment six replicates. The birds were fed basal diet supplemented with 0 and 100 IU/kg vitamin E in the form of DL-α-tocopheryl acetate, respectively. The body weight, carcass performance and IMF content were measured. Transcriptome profile of pectoral muscle in 35-day-old chickens were sequencing from the control and 100 IU/kg vitamin E treatment. Functional enrichment analyzes of differentially expressed genes (DEGs) based on Gene ontology (GO), KEGG pathway and bio function, and network were performed. Results shown that IMF content of broiler chickens were significantly increased at 12.89% (P < 0.05) between 100 IU/kg vitamin E treatment and control. Transcriptome sequencing results for pectoralis major muscle of 100 IU vitamin E-supplemented and the control groups identified 57 up-regulated and 102 down-regulated DEGs. These DEGs were significantly enriched (FDR corrected P-value < 0.05) in 13 of 236 GO terms involved in muscle development- and lipid metabolism. Pathway functional enrichment analysis revealed that the DEGs were significantly enriched in three signalling pathways (FDR corrected P-value < 0.05). Two of them, MAPK signaling pathway and FoxO signaling pathway, play key roles in muscular and lipid metabolism. It is worth mentioning that 46 DEGs were significantly enriched in 28 skeletal and muscular system development and function categories and 31 DEGs were significantly enriched in 17 lipid metabolism function categories. Moreover, three lipid metabolism and muscular development-related networks of DEGs were also identified. These DEGEs, pathways, function categories and networks identified in this study provide us new insights for the vitamin E regulation of the IMF deposition in broiler chickens.
2021-07-08 | GSE179569 | GEO
Project description:Previous reports have shown low vitamin D serum levels and polymorphisms in the vitamin D receptor (VDR) to be associated with increased risk for TB. Given that 1α,25-dihydroxyvitamin D3 has a role in lipid metabolism control, we tested whether the link between 1α,25-dihydroxyvitamin D3 and tuberculosis involves macrophage lipid metabolism. Since formation of lipid droplets (LD) is a hallmark of lipid dysregulation in M. tuberculosis-infected macrophages, we measured LD content as a readout of altered lipid metabolism in infected THP-1 cells. Induction of LD, which peaked by 24 hours post-infection was prevented by addition of 1α,25-dihydroxyvitamin D3 at the time of infection. To investigate the mechanism of 1α,25-dihydroxyvitamin D3 modulation of LD formation, we analyzed the transcriptome of M. tuberculosis-infected THP-1 cells with and without 1α,25-dihydroxyvitamin D3 treatment.
2014-07-01 | GSE57028 | GEO
Project description:Vitamin D deficiency is a risk factor for developing multiple sclerosis (MS). Both in vitro and animal studies suggest an immunomodulatory effect of vitamin D. The PrevANZ trial, a phase IIb randomized placebo-controlled trial of oral vitamin D3 supplementation in people with a first demyelinating event (FDE), was conducted to determine if supplementation can prevent recurrent disease activity in this cohort at high risk of developing definite MS. As a sub-study of this trial, we used whole blood transcriptomic analyses to investigate the effect of vitamin D3 supplementation on peripheral immune cells in people with an FDE, and to gain insight into potential mechanisms by which vitamin D3 may regulate MS risk and disease activity. The PrevANZ trial randomized participants to 1000 IU, 5000 IU or 10,000 IU daily of oral vitamin D3 or placebo. Peripheral blood was collected at baseline and 12 weeks in PAXgene Blood RNA tubes. Transcriptomic datasets were generated by RNA sequencing.
| EGAS00001007346 | EGA
Project description:Optimization of broiler chicken breast muscle protein accretion is key for the efficient production of poultry meat, whose demand is steadily increasing. In a context where antimicrobial growth promoters use is being restricted, it is important to find alternatives as well as to characterize the effect of immunological stress on broiler chicken growth. Despite of its importance, research on broiler chicken muscle protein dynamics has been mostly limited to the study of mixed protein turnover. The present study aims to characterize the effect of a bacterial challenge and the feed supplementation of a citrus and a cucumber extract on broiler chicken individual breast muscle proteins fractional synthesis rates (FSR) using a recently developed dynamic proteomics pipeline. 21 day-old broiler chickens were administered a single 2H2O dose before being culled at different timepoints. A total of 60 breast muscle protein extracts from five experimental groups (Unchallenged, Challenged, Control Diet, Diet 1 and Diet 2) were analyzed using a DDA proteomics approach. Proteomics data was filtered in order to reliably calculate multiple proteins FSR making use of a newly developed bioinformatics pipeline. Broiler breast muscle proteins FSR uniformly decreased following a bacterial challenge, this change was judged significant for 15 individual proteins, the two major functional clusters identified as well as for mixed breast muscle protein. Citrus or cucumber extract feed supplementation did not show any effect on the breast muscle protein FSR of immunologically challenged broilers. The present study has identified potential predictive markers of breast muscle growth and provided new information on broiler chicken breast muscle protein turnover which could be essential for improving the efficiency of broiler chicken meat production.
2024-04-04 | PXD044325 | Pride
Project description:Background: In addition to its canonical functions, vitamin D has been proposed to be an important mediator of the immune system. Despite ample sunshine, vitamin D deficiency is prevalent (> 80%) in the Middle East, resulting in a high rate of supplementation. However, the underlying molecular mechanisms of the specific regimen and potential factors affecting an individual’s response to vitamin D are not well characterized. Objective: To characterize changes in blood transcriptomic and the potential mechanisms associated with vitamin D3 supplementation and response. Design: In this intervention study, one hundred vitamin D-deficient women were given a weekly oral dose (50,000 IU) of vitamin D3 for three months. A high-throughput targeted PCR, composed of 264 genes representing important blood transcriptomic fingerprints in health and disease states, was performed on pre- and post-supplementation blood samples to profile the molecular response to vitamin D3. Multivariate, network, gene ontology, and literature mining analyses were used for the interpretation of the transcriptomic profiling results. Results: We identified 54 differentially expressed genes that were strongly modulated by vitamin D3 supplementation. Network analyses showed significant changes in the immune-related pathways such as TLR4/CD14 and IFN receptors, and catabolic processes related to NFkB, which were subsequently confirmed by gene ontology enrichment analyses. We proposed a model for vitamin D3 response, using the reduced expression of the molecules involved and the receptor-mediated intra-cellular signaling leading to reduce cytokine production. Conclusions: Blood-transcriptomic profiles of vitamin D3 response were generated using a targeted blood gene panel. Vitamin D has a strong effect on the immune system, G-coupled protein receptor signaling, and the ubiquitin system. We highlighted the major molecular changes and biological processes induced by vitamin D3, which will help to further investigate the effectiveness of vitamin D supplementation among individuals in the Middle East.
2021-05-19 | GSE157939 | GEO
Project description:Overfeeding reduces laying performance in broiler breeder hens (Gallus gallus domesticus). To unravel the effect of feeding regimes on energy metabolism and egg production, high-throughput RNA sequencing was utilized to identify differentially expressed genes (DEGs) in ovary, liver and adipose tissues of broiler chickens under ad libitum and restricted feeding. The transcriptome analysis showed that 289, 388 and 204 DEGs were identified in the adipose tissue, liver and ovary, respectively, between ad libitum and restricted feeding groups. Bioinformatics analysis by STRING further revealed DEGs were significantly enriched in phagosome pathway, lipid transport and location biological process, and the molecular function of lipid transporter activity and nutrient reservoir activity in ovary; the pathways of “steroid hormone biosynthesis” and “metabolism of xenobiotics by cytochrome P450”, and the molecular function of nutrient reservoir activity in adipose tissue; the metabolic pathways, Jak-STAT signaling pathway and PPAR signaling pathway in liver.
2019-05-08 | GSE113722 | GEO
Project description:Previous reports have shown low vitamin D serum levels and polymorphisms in the vitamin D receptor (VDR) to be associated with increased risk for TB. Given that 1?,25-dihydroxyvitamin D3 has a role in lipid metabolism control, we tested whether the link between 1?,25-dihydroxyvitamin D3 and tuberculosis involves macrophage lipid metabolism. Since formation of lipid droplets (LD) is a hallmark of lipid dysregulation in M. tuberculosis-infected macrophages, we measured LD content as a readout of altered lipid metabolism in infected THP-1 cells. Induction of LD, which peaked by 24 hours post-infection was prevented by addition of 1?,25-dihydroxyvitamin D3 at the time of infection. To investigate the mechanism of 1?,25-dihydroxyvitamin D3 modulation of LD formation, we analyzed the transcriptome of M. tuberculosis-infected THP-1 cells with and without 1?,25-dihydroxyvitamin D3 treatment. THP-1 cells were cultured in 24-well flat bottom plates, pre-treated with 20ng/ml PMA for 24 h, and incubated with M. tuberculosis H37Rv. After 4 hours of infection, cells were washed to remove extracellular bacteria and treated with 100 nM of 1?,25-dihydroxyvitamin D3. THP-1 cells were collected and analyzed at 24h. 3 biological replicates in each of the 4 groups were prepared: Infected, Infected plus 1?,25-dihydroxyvitamin D3, Non-infected, Non-infected plus 1?,25-dihydroxyvitamin D3.
2014-07-01 | E-GEOD-57028 | biostudies-arrayexpress
Project description:In this study, we investigated the effect of vitamin D supplementation on tumorigenesis in a thioacetamide (TAA)-induced rat intrahepatic cholangiocarcinoma model as vitamin D is known to have a spectrum of anticancer activities. Using PET, we found that tumor formation and progression were suppressed in rats fed a diet supplemented with 6 IU/g vitamin D3(+6D) as compared to the group fed a 2 IU/g vitamin D3 diet (+2D) or controls. Microarray analysis of the tumors that arose revealed that vitamin D supplementation caused significant up- and down regulation in 21 and 16 genes, respectively.
2015-08-01 | GSE48961 | GEO
Project description:In this study, we investigated the effect of vitamin D supplementation on tumorigenesis in a thioacetamide (TAA)-induced rat intrahepatic cholangiocarcinoma model as vitamin D is known to have a spectrum of anticancer activities. Using PET, we found that tumor formation and progression were suppressed in rats fed a diet supplemented with 6 IU/g vitamin D3(+6D) as compared to the group fed a 2 IU/g vitamin D3 diet (+2D) or controls. Microarray analysis of the tumors that arose revealed that vitamin D supplementation caused significant up- and down regulation in 21 and 16 genes, respectively. There are 9 tissue samples (3 rats in each group labeled as (+6), (+2) and control). Duplicate analysis were used for each sample.
2015-08-01 | E-GEOD-48961 | biostudies-arrayexpress
Project description:Slow-growing Korat chicken (KR) is an alternative to broiler chickens that has been used as a national tool to support smallholder farmers due to a higher selling price of KR meat. However, the individual variability of feed efficiency (FE) within a KR stockbreeding results in a lack of competitiveness. Therefore, improvement of FE of KR is of major importance to improve the profitability of livestock production enterprises. Here, we selected two groups of KR with divergent feed conversion ratios (FCR). We performed RNA-sequencing in order to profile KR jejunal transcriptome and to identify the transcriptional variations and biological pathways implied in response to divergent FCR. The biological pathways involved were revealed by enrichment of the Gene Ontology (GO) terms, and the Kyoto Encyclopedia of Gene and Genome (KEGG) pathways. The results showed that main pathways involved in KR FCR divergence were related to immune response, glutathione metabolism, vitamin transport and metabolism, lipid metabolism, and maturation, development and growth. This is the first study to investigate the molecular genetic mechanisms affecting the FCR values in jejunum of slow-growing chicken. This study will be useful in the line-breeding programs for slow growing chickens to improve FE in the stockbreeding and its profitability.
2021-09-29 | GSE178916 | GEO