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Next Generation Sequencing Facilitates Quantitative Analysis of Taurine Promoted Transcriptomes

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of Taurine Promoted Transcriptomes

PROVIDER: PRJNA607531 | ENA |

REPOSITORIES: ENA

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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]

| PRJNA682355 | ENA

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.

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

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

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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

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Next Generation Sequencing Facilitates Quantitative Analysis of CHAA Transcriptomes

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Next Generation Sequencing Facilitates Quantitative Analysis of IBP Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of IBP Transcriptomes

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Next Generation Sequencing Facilitates Quantitative Analysis of Retinoblastoma Transcriptomes

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Next Generation Sequencing Facilitates Quantitative Analysis of Normal Human Kidney Transcriptomes

Project description:Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived normal human kidney transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis The kidney tissue was immediately placed and stored in RNAlater® (Ambion), according to the manufacturer’s instruction. The tissue was manually microdissected under microscope in RNAlater® pool for glomerular and tubular compartment. Dissected tissue was homogenized and RNA was prepared using RNAeasy mini columns (Qiagen, Valencia, CA, US), according to the manufacturer’s instructions. RNA quality and quantity were determined using the Laboratory-on-Chip Total RNA PicoKit Agilent BioAnalyzer. Only samples without evidence of degradation were further used (RNA Integrity Number >6).

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Next Generation Sequencing Facilitates Quantitative Analysis of B cell Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of B cell Transcriptomes

| PRJNA694930 | ENA