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Next Generation Sequencing Facilitates Quantitative Analysis of healthy indiviual and HUWE1-promoted XLID Transcriptomes

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of healthy indiviual and HUWE1-promoted XLID Transcriptomes

PROVIDER: PRJNA540601 | ENA |

REPOSITORIES: ENA

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Next Generation Sequencing Facilitates Quantitative Analysis of healthy indiviual and HUWE1-promoted XLID Transcriptomes

Project description:mRNA profiles of healthy vs HUWE1 mutant cells were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000 (single read, 75bp).

2021-03-06 | GSE130551 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Taurine Promoted Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Taurine Promoted Transcriptomes

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Next Generation Sequencing Facilitates Quantitative Analysis of Taurine Promoted Transcriptomes [Control+DON]

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Taurine Promoted Transcriptomes [Control+DON]

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Next Generation Sequencing Facilitates Quantitative Analysis of Taurine Promoted Transcriptomes

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

Next Generation Sequencing Facilitates Quantitative Analysis of Taurine Promoted Transcriptomes [Control+DON]

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

Next Generation Sequencing Facilitates Quantitative Analysis of Solanum lycopersicum bud and flower Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Solanum lycopersicum bud and flower Transcriptomes

2021-02-27 | GSE164382 | GEO