Next Generation Sequencing Facilitates Quantitative Analysis of Taurine Promoted Transcriptomes [Control+DON]
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA682355 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13191827_1.fastq.gz | Fastqsanger.gz | |||
| SRR13191827_2.fastq.gz | Fastqsanger.gz | |||
| SRR13191828_1.fastq.gz | Fastqsanger.gz | |||
| SRR13191828_2.fastq.gz | Fastqsanger.gz | |||
| SRR13191829_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: DON inhibits the activation of gamadelta T cells. The goals of this study are to identify genes and pathways invovled in the regulation. Methods: Mouse splenic gamadelta T cells were stimulated with IL-23 and IL1β, together with or without DON for 3 days. Then, the next-generation libraries of mRNA were prepared using VAHTS mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme, Nanjing, China). The Library quality was determined by Bioanalyzer 4200 (Agilent, Santa Clara, CA, USA). Then the mRNA-seq libraries were sequenced in HiSeq ⅹ10 system (Illumina, San Diego, CA, USA) on a 150bp paired-end run. The differentially expressed genes were selected as having more than 1 fold difference in their geometrical mean expression between the compared groups and a statistically significant p-value (<0.05) by analysis of DEseq2. The GO analysis on differentially expressed genes was performed with an R package: Clusterprofiler using a p<0.05 to define statistically enriched GO categories. Pathway analysis was used to determine the significant pathway of the differential genes according to Kyoto Encyclopedia of Genes and Genomes Database (http://www.genome.jp/kegg/), the enrichr database (https://maayanlab.cloud/Enrichr/) and DAVID Bioinformatics Resources 6.8 (https://david.ncifcrf.gov/). Results: Genes in the IL-23/STAT3 pathway were inhibited by taurine. As a result, the production of IL-17A decreased upon DON treatment.
2020-12-04 | GSE162598 | GEO
Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Taurine Promoted Transcriptomes
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Project description:Purpose: Taurine promotes the activation of plasmacytoid dendritic cells. The goals of this study are to identify genes and pathways invovled in the regulation. Methods: Mouse plasmacytoid dendritic cells were stimulated with R837, together with or without taurine for 12 hours. Then, the next-generation libraries of mRNA were prepared using VAHTS mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme, Nanjing, China). The Library quality was determined by Bioanalyzer 4200 (Agilent, Santa Clara, CA, USA). Then the mRNA-seq libraries were sequenced in HiSeq ⅹ10 system (Illumina, San Diego, CA, USA) on a 150bp paired-end run. The differentially expressed genes were selected as having more than 1 fold difference in their geometrical mean expression between the compared groups and a statistically significant p-value (<0.05) by analysis of DEseq2. The GO analysis on differentially expressed genes was performed with an R package: Clusterprofiler using a p<0.05 to define statistically enriched GO categories. Pathway analysis was used to determine the significant pathway of the differential genes according to Kyoto Encyclopedia of Genes and Genomes Database (http://www.genome.jp/kegg/) and DAVID Bioinformatics Resources 6.8 (https://david.ncifcrf.gov/). Results: Genes in the TLR7-IRF7 pathway were augmented by taurine. As a result, the production of type I IFNs increased upon taurine treatment.
2020-02-20 | GSE145546 | GEO
Project description:Next Generation Sequencing Facilitates Quantitative Analysis of healthy indiviual and HUWE1-promoted XLID Transcriptomes
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Project description:To identify molecular characteristics of WT AM with or without DON stimulation in vitro, we isolated RNA from AMs with various treatments and examined by bulk RNA-seq. We found a large number of gene profiles were altered following DON treatment in WT AMs, suggesting that DON treatment altered the balance of proliferative versus inflammatory genes in AMs, and glutamine metabolism is important in regulating AM self-renewal ability.
2023-12-31 | GSE210076 | GEO
Project description:Deoxynivalenol (DON) is a frequent mycotoxin in grains, produced by Fusarium fungi, which demonstre multiple side effects such as modulation of immune responses, reduced feed intake and weight gain or impairment of the intestinal barrier function. Among animal species, pigs are the best model for humans and are very sensitive to DON. In wheat, DON can be conjugated to glucose to form DON-3-β-D-glucoside (D3G). Some bacteria isolated from digestive tracts or soil, are also able to de-epoxydize or epimerize DON to metabolites such as deepoxy-deoxynivalenol (DOM-1) or 3-epi-deoxynivalenol (epi-DON). The toxicity of these DON metabolites is poorly documented. By the way of ingestion, the intestine is the first organ exposed to these molecules and so constitute a relevant model. The aim of this study was to compare the intestinal toxicity of three DON metabolites (D3G, DOM-1 and epi-DON) with the one of DON. Intestinal explants from 6 pigs were treated with 10mM DON, D3G, DOM-1 or epi-DON for 4 hours and transcriptomic analysis was performed using an “Agilent Porcinet 60K”.
2016-07-20 | GSE66918 | GEO
Project description:Background: Metabolic dysregulation has been implicated in bronchopulmonary dysplasia development. Taurine is an essential amino acid for neonates and is critically involved in glucose and fatty acid metabolism. Neonatal tissue obtains taurine mainly through the taurine transporter. The biological role of taurine in neonatal lung development has never been explored. As glucose metabolism mechanistically modulates angiogenesis and angiogenesis is the central player for neonatal lung development, we hypothesize that taurine depletion contributes to bronchopulmonary dysplasia development. Results: Although most genes and proteins for oxidative phosphorylation were enriched in hyperoxia pup lungs, the complex-1 activity decreased. The decrease in taurine-dependent complex-1 core subunits, ND5 and ND6, in hyperoxia lungs reasonably explained the discrepancy. Metabolomics analysis demonstrated decreased lung taurine with increased blood taurine of hyperoxia pups, compatible with the decreased taurine transporter expression. Decreased glycosylation and increased degradation explained the decreased taurine transporter expression. The results of the complementary study using tunicamycin and tauroursodeoxycholic acid studies supported that endoplasmic reticulum stress contributes to decreased taurine transporter expression in hyperoxia lungs. The effect of taurine treatment on reducing endoplasmic reticulum stress, increasing ND5 and ND6 expression, angiogenesis, and, most importantly, the alveolar formation is beneficial to hyperoxia rat pups. Conclusion: Hyperoxia exposure causes endoplasmic reticulum stress, increases taurine transporter degradation, and leads to taurine depletion in the neonatal lungs with subsequent metabolic dysregulation, resulting in poor alveolar formation of the neonatal lungs. We provide evidence of the never-being-reported protective role of taurine in neonatal lung development. The fact that taurine attenuates the severity of bronchopulmonary dysplasia by reducing hyperoxia-induced endoplasmic reticulum stress and mitochondrial dysfunction indicates its therapeutic potential for treating bronchopulmonary dysplasia.
2024-06-01 | GSE249767 | GEO
Project description:Deoxynivalenol (DON) is a frequent mycotoxin in grains, produced by Fusarium fungi, which demonstre multiple side effects such as modulation of immune responses, reduced feed intake and weight gain or impairment of the intestinal barrier function. Among animal species, pigs are the best model for humans and are very sensitive to DON. In wheat, DON can be conjugated to glucose to form DON-3-β-D-glucoside (D3G). Some bacteria isolated from digestive tracts or soil, are also able to de-epoxydize or epimerize DON to metabolites such as deepoxy-deoxynivalenol (DOM-1) or 3-epi-deoxynivalenol (epi-DON). The toxicity of these DON metabolites is poorly documented. By the way of ingestion, the intestine is the first organ exposed to these molecules and so constitute a relevant model. The aim of this study was to compare the intestinal toxicity of three DON metabolites (D3G, DOM-1 and epi-DON) with the one of DON. Intestinal explants from 6 pigs were treated with 10mM DON, D3G, DOM-1 or epi-DON for 4 hours and transcriptomic analysis was performed using an âAgilent Porcinet 60Kâ. Jejunal explants from 4 piglets aged of 5 weeks were sampled and exposed in vitro to differents molecules (DON, D3G, DOM-1 & 3-epi-DON) at 10µM during 4h. Then RNA was extracted.
2016-07-20 | E-GEOD-66918 | biostudies-arrayexpress
Project description:Analysis of skeletal muscle from taurine transporter (TauT) knockout mice at 3 or 18 months of age. Knocking out TauT result in a decrease in muscle cell size, impaired exercise capacity and accelerated muscle aging. Results provide molecular insights into physiological role of taurine. Sample: 12
2014-05-08 | E-GEOD-57373 | biostudies-arrayexpress
Project description:Analysis of skeletal muscle from taurine transporter (TauT) knockout mice at 3 or 18 months of age. Knocking out TauT result in a decrease in muscle cell size, impaired exercise capacity and accelerated muscle aging. Results provide molecular insights into physiological role of taurine.
2014-05-08 | GSE57373 | GEO