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Transcriptomic analysis of peritoneal macrophages from MED1 fl/fl and macrophage MED1 KO mice

ABSTRACT: Transcriptomic analysis of peritoneal macrophages from MED1 fl/fl and macrophage MED1 KO mice

PROVIDER: PRJNA806841 | ENA |

REPOSITORIES: ENA

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Transcriptomic analysis of peritoneal macrophages from MED1 fl/fl and macrophage MED1 KO mice

Project description:Purpose: The goal of this study is to obtain the differential gene expression in MED1fl/fl and MED1ΔMac peritoneal macrophages (PMs) stimulated with or without LPS. Methods: Pooled PMs were collected from 8-week-old MED1fl/fl and MED1ΔMac mice (n=6 mice/group), and then treated without or with lipopolysaccharide (LPS; 50 ng/mL) for 6 hours. PMs mRNA profiles were generated by deep sequencing, in duplicate, using Illumina NextSeq500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: reads were mapped to the mm9 whole genome using tophat and RPKM were calculated using cufflink. qRT–PCR validation was performed using SYBR Green assays. Results: Using an optimized data analysis workflow, we mapped about 12 million sequence reads per sample to the mouse genome (build mm9) and identified 24,130 transcripts in the PMs of MED1fl/fl and MED1ΔMac mice. Data analysis with TopHat and Cufflinks workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling. Conclusions: Our study represents the detailed analysis of PMs transcriptomes, with biologic replicates, generated by RNA-seq technology. Our results show that the expression of more than 20 genes involved in innate immune response and M1 polarization was significantly higher in MED1ΔMac than in MED1fl/fl macrophages after LPS treatment. Upregulated genes in MED1ΔMac macrophages are the proinflammatory genes.

2022-02-17 | GSE196680 | GEO

Project description:Transcriptomic analysis of peritoneal macrophages from MED1 fl/fl and macrophage MED1 KO mice

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Bone marrow derived macrophage vs peritoneal macrophage

Project description:Bone marrow derived macrophage vs peritoneal macrophage

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Precision N-glycoproteomics of murine peritoneal macrophage

Project description:In this study, we profiled the precision N-glycoproteome of the murine peritoneal macrophage under different stimulation.

2021-06-12 | PXD026629 | Pride

Single cell RNA sequencing of peritoneal cells from macrophage-Cd36-/- and macrophage-Cd36 fl/fl mice at the resolution phase of sterile inflammation.

Project description:Monocytes and macrophages as components of innate immunity are critical for both homeostasis and inflammation. The scavenger receptor CD36, highly expressed in macrophages, promotes immunological responses mediated by recognition of molecular patterns on pathogens or endogenous ligands on apoptotic cells. CD36 mediated lipid uptake also allows metabolic adaptations that influence macrophage phenotype and polarization. CD36 binds diverse lipids including fatty acids and various lipoproteins, which could exert differential effects on macrophage conversion. Previous studies reported opposite outcomes due to CD36-mediated lipid uptake; macrophages converted to either an inflammatory or an alternatively activated phenotype. To determine the role of this receptor in vivo in the presence of physiological lipid sources, we created macrophage-specific CD36 knockout mice. Using zymosan-induced peritonitis to activate immune cells, we show through single cell RNA sequencing analysis that a broad variety of resident and infiltrated immune cells are present in the peritoneum 72h after the initial stimulus. CD36 deficiency did not affect the numbers of cells during the infiltration and resolution phases, but CD36 deficiency altered the macrophage transcriptome. Pathways related to innate immunity, antigen presentation and oxidative phosphorylation were upregulated in macrophages with CD36 deficiency, whereas those related to efferocytosis, adaptive immunity and B cell activation were downregulated. Despite these gene changes, neither immunoglobulin production nor peritoneal efferocytosis was altered by macrophage CD36 deficiency, nor were there changes in the numbers of circulating white blood cells. Thus, CD36 deficiency does not reduce the inflammatory phenotype of induced peritoneal macrophages.

2024-05-31 | GSE210795 | GEO

mRNAseq and proteomic data set of one week old WT (Chop wt/wt CkmmCre wt/wt Dars2 fl/fl), Chop KO (Chop ko/ko CkmmCre wt/wt Dars2 fl/fl), Dars2 KO (Chop wt/wt CkmmCre tg/wt Dars2 fl/fl) and DKO (Chop ko/ko CkmmCre tg/wt Dars2 fl/fl) mice

Project description:mRNAseq and proteomic data set of one week old WT (Chop wt/wt CkmmCre wt/wt Dars2 fl/fl), Chop KO (Chop ko/ko CkmmCre wt/wt Dars2 fl/fl), Dars2 KO (Chop wt/wt CkmmCre tg/wt Dars2 fl/fl) and DKO (Chop ko/ko CkmmCre tg/wt Dars2 fl/fl) mice

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Genome-wide analysis of LPS or PBS challenged DUSP3-KO and WT female mice peritoneal macrophages gene expression

Project description:Analysis of gene expression profile in peritoneal macrophage extracted from LPS or PBS challenged DUSP3-/- and WT mice. DUSP3 deletion protects mice from sepsis and endotoxemia. We performed a microarray analysis to get insights into the differentially regulated pathways between WT and KO under inflammatory conditions. Total RNA obtained from isolated peritoneal macrophages isolated from DUSP3-/- and WT mice 36 hours after challenging them in vivo with PBS or with 6mg/kg of LPS.

2015-03-11 | E-GEOD-66782 | biostudies-arrayexpress

Med1 overexpression induces cell proliferation

Project description:Med1 overexpression leads to induction of a wide spectrum of genes. Adenovirally-driven overexpression of Med1 in mouse liver stimulates hepatocyte DNA synthesis with enhanced expression of DNA replication, cell cycle control and liver specific genes as observed at day 3 and day 5 post injection. Med1 gene is amplified in a number of cancers so in this study we tested the hypothesis that Med1 by itself has the capacity to induce cell proliferation. Analysis of the Med1- induced gene expression showed a robust induction of a wide spectrum of genes involved in hepatocellular proliferation. Med1 floxed mice (Med1fl/fl) were injected with Ad-His-Med1 (adenovirus expressing Med1 gene) via tail vein and killed 3 or 5 days after injection. Ad-LacZ (adenovirus expression beta-galactosidase gene) injected mouse liver served as control. Total RNA were isolated from the liver and subjected to the microarray.

2013-07-18 | E-GEOD-48950 | biostudies-arrayexpress

Genome-wide analysis of LPS or PBS challenged DUSP3-KO and WT female mice peritoneal macrophages gene expression

2015-03-11 | GSE66782 | GEO

Expression data from peritoneal macrophages stimulated with lipid A

Project description:Setdb1 is one of the H3K9 methyltransferases and represses gene expression by H3K9 methylation. In an attempt to elucidate the role of Setdb1 in the TLR4-mediated inflammatory responses, we performed DNA microarray analysis using lipid A (the active component of LPS)-stimulated peritoneal macrophages from macrophage specific Setdb1 KO (KO) and WT mice. The genes upregulated by lipid A treatment in WT macrophages and further increased in KO macrophages contain many genes associated with interleukins and chemokines. Peritoneal macrophages from WT and KO mice were stimulated with lipid A 10 ng/ml or vehicle for 4 h. Microarray analysis was performed using Affymetrix Mouse 430 2.0.

2016-06-27 | E-GEOD-78153 | biostudies-arrayexpress

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