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Next Generation Sequencing Facilitates Quantitative Analysis of MED23-knockdown and Control HUVEC Cells Transcriptomes

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of MED23-knockdown and Control HUVEC Cells Transcriptomes

PROVIDER: PRJNA772680 | ENA |

REPOSITORIES: ENA

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Next Generation Sequencing Facilitates Quantitative Analysis of MED23-knockdown and Control HUVEC Cells Transcriptomes

Project description:Purpose: RNA-seq analysis to evaluate the impact of MED23 knockdown on the transcriptome of HUVEC cells.Methods: Total RNA was isolated with TRIzol from Med23 knockdown HUVECs (n = 3) or control cells (n = 3). cDNA sequencing libraries were prepared with an NEBNext® Ultra™ RNA Library Prep Kit for Illumina. The RNA-Seq FASTQ raw data were trimmed to remove low-quality reads and adapters using Trimmomatic. The trimmed reads were aligned to the mouse reference genome UCSC GRCh37/hg19 with HISAT2. Gene and transcript quantification was performed using Cutdiff. The results of the mapping of the RNA-seq reads, transcript assembly and abundance estimation were reported as fragments per kilobase of exon per million fragments mapped (FPKM).

2021-10-21 | GSE186112 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of P. gingivalis and HUVEC Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of P. gingivalis and HUVEC Transcriptomes

| PRJNA763155 | ENA

The Mediator MED23 plays opposing roles in directing smooth muscle cell and adipocyte differentiation

Project description:The Mediator complex functions as a control center orchestrating diverse signalings, gene activities, and biological processes. However, how Mediator subunits determine distinct cell fates remains to be fully elucidated. Here, we show that Mediator MED23 controls the cell fate preference that directs differentiation into smooth muscle cells (SMCs) or adipocytes. Med23-deficiency facilitates SMC differentiation but represses adipocyte differentiation from the multipotent mesenchymal stem cells. Gene profiling revealed that the presence or absence of Med23 oppositely regulates two sets of genes: the RhoA/MAL-targeted cytoskeleton/SMC genes and the Ras/ELK1 targeted growth/adipocyte genes. Mechanistically, MED23 favors ELK1-SRF binding to SMC gene promoters for repression, whereas the lack of MED23 favors MAL-SRF binding to SMC gene promoters for activation. Remarkably, the effect of MED23 on SMC differentiation can be recapitulated in zebrafish embryogenesis. Collectively, our data demonstrate the dual, opposing roles for MED23 in regulating the cytoskeleton/SMC and growth/adipocyte gene programs, suggesting its “Ying-Yang” function in directing adipogenesis vs. SMC differentiation. Examination of SRF enrichment in sictrl and si23 10T1/2 cells

2012-12-20 | E-GEOD-40369 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of adipose tissue Treg and LN Treg Transcriptomes

Project description:The goal of this study is to reveal unique features of adipose Tregs and to study mechanisms underlying how mediator Med23 regulate adipose Treg function in aged mice. Therefore, mRNA profiles of LN Tregs (from 4-month old Foxp3Cre mice) and adipose Tregs (from 4-month old Foxp3Cre, 4-month old obese Foxp3Cre, 10-month old Foxp3Cre and 10-month old Med23fl/fl;Foxp3Cre mice) were generated by deep sequencing, single experiment, using Illumina HiSeq2000. We compared transcriptome features between lymph node-derived Tregs and adipose Tregs from 4-month old lean or obese mice. Using unbiased comparative gene expression analyses, we found adipose Tregs display an up-signature of Insr (Insulin receptor) and Hif1a, while Pparg acts as a positive control. We next compared gene expression profiles of adipose Tregs from 10-month old Med23fl/fl;Foxp3Cre (MKO) and Foxp3Cre (WT) mice. adipose Med23-ΔTreg cells display impaired transcription of Pparg and Il1rl1 (ST2), and they simultaneously acquire the expression of Nt5e (CD73), while Entpd1 (CD39) expression was not dramatically altered. Our studies implicate protective roles of CD73hi adipose Tregs and offer new therapeutic strategies against age-associated metabolic syndrome.

2021-07-15 | GSE124721 | GEO

The Mediator MED23 plays opposing roles in directing smooth muscle cell and adipocyte differentiation

2012-12-20 | GSE40369 | GEO

Quantitative Analysis of mRNA expression in calvaria tissue from control and Med23-/- vs. wild type and Runx2+/- mice through Next Generation Sequencing

Project description:We sequenced mRNA from 12 single newborn mouse calvaria tissues ( from 3 control and 3 Med23-/- cKO mice from a litter; 3 wildtype and 3 Runx2+/- mice from another litter) to investigate the correlation between Med23 and Runx2 in terms of affect on the mRNA level by their deficiencies. We find there is a positiove correlation in gobal gene expression affected by defiencies of the two genes.

2016-01-21 | GSE77007 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of P. gingivalis and HUVEC Transcriptomes

Project description:Purpose: This study provides the transcriptional landscape of intracellular P. gingivalis as well as that of endothelial cells infected by this bacteria based on dual RNA sequencing. Methods: HUVECs were seeded in 6-well plates and cultured to 80% confluence. After washing with phosphate-buffered saline (PBS), cell were infected with P. gingivalis at a multiplicity of infection (MOI) of 100 for 2 h at 37 °C in 5% CO2, unless otherwise stated. Non-adherent bacteria were removed by washing with PBS, and the cell-adherent bacteria were killed using gentamicin (300 μg/mL) and metronidazole (200 μg/mL) for 1 h at 37 °C in 5% CO2.Total RNA was isolated from the samples using TRIzol® reagent.cDNA libraries for Illumina® sequencing were generated using the KC-DigitalTM Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA). The library products corresponding to 200–250 bps were then enriched, quantified, and sequenced using a Nova-seq 6000 sequencer (Illumina, San Diego, CA, USA). Results: Using an optimized data analysis workflow, intracellular P. gingivalis showed a total of 573 DEGs compared with the control bacteria, and of these DEGs, 304 and 269 were upregulated and downregulated, respectively. A total of 838 DEGs were detected in P. gingivalis-infected HUVECs compared with their uninfected counterparts, and of these, 297 and 541 genes were upregulated and downregulated, respectively. Conclusions: This study firstly provides the transcriptional landscape of intracellular P. gingivalis as well as that of endothelial cells infected by this bacteria based on dual RNA sequencing.

2021-09-17 | GSE184085 | 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

Med23-dependent gene expression programs in T cells

Project description:To analysis TCR induced Med23-dependent gene expression programs in T cells, we have employed microarray expression profiling as a discovery platform to identify genes with the potential to be regulated by Med23 in unstimulated or stimulated T cells. Mice CD4 T cells from wildtype and Med23 knockout mice were left unstimulated or stimulated for 6 hr, and gene expression difference was identified among four samples. Expression of seven genes (Med23, IFNg, IL2, Egr2, c-Fos, c-Jun and Foxp1) was validated in the same RNA samples by real-time PCR. TCR induced Med23-dependent gene expression was measured after unstimulation or stimulation for 6 hr in wildtype and Med23 knockout CD4 T cells.

2014-08-27 | E-GEOD-60779 | biostudies-arrayexpress

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