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Next Generation Sequencing Facilitates Quantitative Analysis of Spermidine Inhibited Transcriptomes

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of Spermidine Inhibited Transcriptomes

PROVIDER: PRJNA597047 | ENA |

REPOSITORIES: ENA

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Next Generation Sequencing Facilitates Quantitative Analysis of Spermidine Inhibited Transcriptomes

Project description:Purpose: Spermidine inhibits the activation of interferon primed dendritic cells. The goals of this study are to identify genes and pathways invovled in the regulation. Methods: Mouse monocyte derived dendritic cells were primed with interferon α for 24 hours, and then cultured with R837, together with or without spermidine for 18 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 JAK/STAT pathway and the NF-κB pathway were inhibited by spermidine. As a result, the pro-inflammatory cytokines including IL-1β, IL-12a, IL-12b (IL-12/23 p40), IL-6 and IL-23a decreased obviously upon spermidine treatment

2019-12-21 | GSE142452 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of MicroRNA-148a Inhibited Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of MicroRNA-148a Inhibited Transcriptomes

| PRJNA597230 | ENA

Next Generation Sequencing Facilitates Quantitative Analysis of MicroRNA-148a Inhibited Transcriptomes

Project description:Purpose: MicroRNA-148a regulates the differentiation of dendritic cells. The goals of this study are to identify genes and pathways invovled in the regulation. Methods: Monocytes isolated from wild type or microRNA-148a-/- BM were cultured with GM-CSF and IL-4, or not. Cells were collected at day 0 and day 3. 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 0.5 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: Gene ontology analysis showed that obviously changed genes enriched in autoimmune disease related pathways, suggesting miR-148a is important in autoimmune responses. 990 protein-coding genes upregulated in their mRNA abundance in miR-148a-/- monocytes on day 0, and 1036 genes in miR-148a-/- monocytes on day 3. Among them, 136 genes were found upregulation on both day 0 and 3 in miR-148a-/- monocytes.

2019-12-23 | GSE142511 | GEO

Next-generation sequencing facilitates quantitative analysis of wild-type and Nrl(-/-) retinal transcriptomes.

Project description: Not available

| S-EPMC3233386 | biostudies-literature

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

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).

2014-08-06 | E-GEOD-60119 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of Hedgehog Signaling Blockade on Macrophage Transcriptomes

Project description:Purpose: The goal of this study is to compare transcriptome profiling (RNA-seq) between macrophages inhibited for Hedgehog signaling and vehicle control.

2021-11-10 | GSE146223 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of wild-type and erf4 mutant Transcriptomes

Project description:Analysis of gene expression level. The hypothesis tested in the present study was that erf4 mutant affects PMEI genes expression which inhibited PME activity in the seed coat mucilage

2022-12-31 | GSE157508 | GEO