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

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

PROVIDER: PRJNA597230 | ENA |

REPOSITORIES: ENA

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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 Spermidine Inhibited Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Spermidine Inhibited Transcriptomes

| PRJNA597047 | ENA

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

Quantitative Proteomics of miR-148a in gastric cancer cells

Project description:A quantitative proteomics combined with stable isotope labeling was applied to identify the global profile of miR-148a-regulated downstream proteins in AGS cancer cells. For proteomic analysis, cells were treated with miR-148a mimic (Pre-miR-148a) or miR-148a negative control (miR-CTL) and the downstream protein expression level (Pre-miR-148a/miR-CTL) were quantified using iTRAQ approach. Bioinformatics pipeline: The peak list in the resultant MS/MS spectra were generated by Mascot Distiller v2.1.1.0 and searched using Mascot v2.2 against the International Protein Index (IPI) human database (v. 3.64, 84032 sequences). The Mascot search parameters were +-0.1 Da for MS tolerance, +-0.1 Da for MS/MS mass tolerance, allowances for two missed cleavages, and variable modifications of deamidation (NQ), oxidation (M), iTRAQ (N terminal), iTRAQ (K), and MMTS (C). Protein quantitation were calculated using the Multi-Q software v1.6.5.4 with a dynamic range filter of ion count > 30.

2013-07-24 | PXD000190 | Pride

Next Generation Sequencing Facilitates Quantitative Analysis of Changed MicroRNAs in Psoriasis Patients.

Project description:Purpose: MicroRNAs are small noncoding RNAs involved in autoimmune diseases. The goals of this study are to identify changed miRNAs in the peripheral blood mononuclear cell (PBMC) of psoriasis patients. 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 | GSE142510 | 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

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

Project description: Not available

| S-EPMC3233386 | biostudies-literature

MicroRNA-148a-3p in pericyte-derived extracellular vesicles improves erectile function in diabetic mice by promoting cavernous neurovascular regeneration

Project description:Purpose: To investigate the regulatory role of microRNA (miR)-148a-3p in mouse corpus cavernous pericyte (MCPs)-derived extracellular vesicles (EVs) in the treatment of diabetes-induced erectile dysfunction (ED). Materials and Methods: Mouse corpus cavernous tissue was used for MCPs primary culture and EVs isolation. Small RNA sequencing analysis was performed to assess the type and content of miRs in MCPs-EVs. Four groups of mice were used: control nondiabetic mice and streptozotocin-induced diabetic mice receiving two intracavernous injections (days -3 and 0) of phosphate buffered saline, MCPs-EVs transfected with regent control, or MCPs-EVs transfected with miR-148a-3p inhibitor. The function of miR-148a-3p in MCPs-EVs was evaluated by tube formation assay, migration assay, TUNEL assay, intracavernous pressure, immunofluorescence staining, and western blot experiments. Results: We extracted EVs from MCPs and by small RNA sequencing analysis we found that miR-148a-3p is enriched in MCPs-EVs. Exogenous administration of MCPs-EVs can effectively promote mouse cavernous endothelial cell (MCECs) tube formation, migration, proliferation, and reduce MCECs apoptosis under high-glucose conditions. However, these effects are significantly attenuated in miR-148a-3p-depleted MCPs-EVs, which is extracted after inhibiting miR-148a-3p expression in MCPs. Repeated intracavernous injections of MCPs-EVs improves erectile function by inducing cavernous neurovascular regeneration in diabetic mice. Through online bioinformatics databases and luciferase report assays, we predict Pyruvate dehydrogenase kinase-4 (PDK4) is a potential target gene of miR-148a-3p. Conclusions: Our findings provide new and reliable evidence that miR-148a-3p in MCPs-EVs significantly enhances cavernous neurovascular regeneration by inhibiting PDK4 in diabetic mice.

2023-12-19 | GSE195533 | GEO

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

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