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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptome profile of murine bone marrow-derived macrophages treated with 15d-PGJ2 or 15d-PGJ2-PC

ABSTRACT: Purpose: The goal of this study is to investigate the alteration of gene expression pattern induced by 15d-PGJ2 or 15d-PGJ2-PC in BMDMs. Method: BMDMs obtained from C57BL/6 mice were treated with 15d-PGJ2, 15d-PGJ2-PC or media control for 6h. Then RNA sequence was generated by using the Illumina system. Results: Using an optimized data analysis workflow, we mapped about 13 million sequence reads per sample to the mouse genome and identified about 14,500 transcripts in the macrophage mRNAs. Among them, 719 and 286 genes were differentially expressed in 15d-PGJ2 and 15d-PGJ2-PC group respectively. Conclusions: Deoxy-A2/J2-IsoP-PC are a novel series of oxidation products we identified in atherosclerotic plaques. 15d-PGJ2-PC is a representative compound of these oxidation products we chemically synthesised. Using RNA-seq technology, we provided 15d-PGJ2-PC induced gene expression profile and could contribute to study the roles of these novel oxidation products in the atherosclerosis. mRNA profiles of BMDMs from C57B/L6 mice were generated by deep sequencing, in triplicate, using Illumina.

ORGANISM(S): Mus musculus

SUBMITTER: Huiyong Yin

PROVIDER: E-GEOD-85931 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptome profile of murine bone marrow-derived macrophages treated with 15d-PGJ2 or 15d-PGJ2-PC

Project description:Purpose: The goal of this study is to investigate the alteration of gene expression pattern induced by 15d-PGJ2 or 15d-PGJ2-PC in BMDMs. Method: BMDMs obtained from C57BL/6 mice were treated with 15d-PGJ2, 15d-PGJ2-PC or media control for 6h. Then RNA sequence was generated by using the Illumina system. Results: Using an optimized data analysis workflow, we mapped about 13 million sequence reads per sample to the mouse genome and identified about 14,500 transcripts in the macrophage mRNAs. Among them, 719 and 286 genes were differentially expressed in 15d-PGJ2 and 15d-PGJ2-PC group respectively. Conclusions: Deoxy-A2/J2-IsoP-PC are a novel series of oxidation products we identified in atherosclerotic plaques. 15d-PGJ2-PC is a representative compound of these oxidation products we chemically synthesised. Using RNA-seq technology, we provided 15d-PGJ2-PC induced gene expression profile and could contribute to study the roles of these novel oxidation products in the atherosclerosis.

2016-08-24 | GSE85931 | GEO

Electrophilic lipid mediator 15-deoxy-M-NM-^T12,14-prostaglandin J2 modifies glucocorticoid signaling via receptor SUMOylation

Project description:Cortisol, the central stress hormone in humans, activates the glucocorticoid receptor (GR). Anti-inflammatory effects are the most important pharmaceutical effects mediated by the GR. Inasmuch as electrophilic cyclopentenone prostaglandin 15-deoxy-M-NM-^T12,14-prostaglandin J2 (15d-PGJ2) has potent anti-inflammatory properties and activates the SUMOylation pathway, we have investigated the effect of 15d-PGJ2 on glucocorticoid signaling and receptor SUMOylation. To this end, we studied isogenic HEK293 cells expressing either wild-type GR or SUMOylation-defective GR. Interestingly, 15d-PGJ2 triggered SUMO-2/3 modification in the primary SUMOylation sites of the GR. Gene expression profiling and pathway analyses indicate that 15d-PGJ2 inhibits GR signaling in a genome-wide fashion that is significantly dependent on the GR SUMOylation sites. Chromatin immunoprecipitation assays showed that the repressive effect of 15d-PGJ2 on GR target gene expression occurs in parallel with the inhibition of receptor binding to the target gene chromatin. Furthermore, depletion of the sole SUMO E2 conjugase UBC9 from HEK293 cells confirmed the involvement of active SUMOylation in the regulatory process. Taken together, our data indicate that GR SUMOylation modulates the glucocorticoid signaling during acute cell stress. Our data also suggest that GR SUMOylation modulates crosstalk of the glucocorticoid signaling with other transcription factors that are responsive to cell stress. Total RNA isolated from isogenic HEK293 cell lines stably expressing either wild-type GR (wtGR) or SUMOylation-defective GR (GR3KR) treated with 100 nM of dexamethasone (dex) in the presence or absence of 5 M-BM-5M 15d-PGJ2 for 6h. All conditions are performed in triplicate

2014-06-30 | E-GEOD-54087 | biostudies-arrayexpress

Expression analysis of Kit+ derived from wild type C57B/L6 Mouse bone marrow cells Transduced with CSF3R mutants by RNA seq.

Project description:We performed whole genome expression analysis of Kit+ derived from wild type C57B/L6 Mouse bone marrow cells Trabsduced with control vector and CSF3R mutants by RNA seq.

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Single cell sequencing of mouse retina

Project description:Purpose: The goals of this study are to study the expression of Sfxn3 in C57B/L6 mouse retina and retinal cell types Methods: Library prepared followed by 10X Genomics standard protocol. Transcriptome were generated by high throughput sequencing

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2019-10-01 | E-MTAB-8168 | biostudies-arrayexpress

Transcription profiling of mouse stromal cell compartment, lineage negative, CD45 negative bone marrow cells from C57B/L6 and B6.SJL (Ly5.1) strains

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2010-01-20 | E-TABM-829 | biostudies-arrayexpress

Project description:Mouse intestinal microbiota C57B/L6 ICL 2019

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2023-09-01 | GSE237328 | GEO

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Project description:Mus musculus strain:c57b/l6 | breed:eukaryotic Raw sequence reads

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Expression data from the aortas of ApoE knockout, ApoE/Caspase-1 double knockout, and wild-type mice

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