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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and cd36-/- murine peritoneal macrophage Transcriptomes

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and cd36-/- murine peritoneal macrophage Transcriptomes

PROVIDER: PRJNA579834 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10352136_1.fastq.gz	Fastqsanger.gz
	SRR10352136_2.fastq.gz	Fastqsanger.gz
	SRR10352137_1.fastq.gz	Fastqsanger.gz
	SRR10352137_2.fastq.gz	Fastqsanger.gz
	SRR10352138_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and cd36-/- murine peritoneal macrophage Transcriptomes

Project description:Oxidized LDL induce macrophages to turn into foam cells in a CD36 dependent manner. The Goal of this study is to compare transcriptome profile by RNA-seq among WT/CD36 knockout macrophages treated with or without oxLDL. We detected re-organization of lipid metabolisms as well as immune activation by oxLDL.

2019-10-28 | GSE139439 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Peritoneal Macrophage Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Peritoneal Macrophage Transcriptomes

| PRJNA512475 | ENA

Next Generation Sequencing Facilitates Quantitative Analysis of Peritoneal Macrophage Transcriptomes

Project description:Purpose:The purpose of this study is to detect activated or silenced genes during KAT8-deficient peritoneal macrophages and the control cells. Gene expression differences between two samples could be found using transcriptome profiling (RNA-seq) analysis. Methods:Mouse peritoenal macrophages were harvested from mice 3 days after thioglycollate (Merck) injection. Macrophages RNA profiles were generated by deep sequencing,using Illumina. Results: We mapped about 10 million sequence reads per sample to the mouse genome, identified hundreds of genes with significant mRNA variation between KAT8-deficient macrophages and the control cells.

2019-01-03 | GSE124551 | GEO

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

Next-Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Kdm2b-/- Peritoneal Macrophage Transcriptomes

Project description:Purpose: The purpose of this study is to detect activated or silenced genes during Kdm2b-deficient peritoneal macrophages and the control cells. Gene expression differences between two samples could be found using transcriptome profiling (RNA-seq) analysis. Methods: Mouse peritoneal macrophages were harvested from mice 4 days after thioglycollate (BD, Sparks, MD) injection. Macrophages RNA profiles were generated by deep sequencing, using Illumina. Results: We mapped about 10 million sequence reads per sample to the mouse genome, identified hundreds of genes with significant mRNA variation between Kdm2b-deficient macrophages and the control cells.

2019-12-31 | GSE120651 | GEO

Next-Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Kdm2b-/- Peritoneal Macrophage Transcriptomes

Project description:Next-Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Kdm2b-/- Peritoneal Macrophage Transcriptomes

| PRJNA493834 | ENA

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and α7nAChR-/- Peritoneal macrophage Transcriptomes with Nicotine and/or LPS treatment

Project description:Purpose: The cholinergic anti-inflammatory pathway (CAP) links the nervous and immune systems and modulates innate and adaptive immunity. The goals of this study are to identify the new downstream signaling of α7nAChR in macrophages. Methods: Peritoneal macrophages isolated from α7nAChR+/+ and α7nAChR-/- mice were treated with nicotine (10 μM) and/or LPS (100 ng/ml), then RNA-seq was performed. Results: Genes were selected that had more than 4-fold relative gene expression in nicotine-treated cells compared to the control group (vehicle-treated). The same calculation was applied to nicotine+LPS-treated cells and LPS-treated cells and 264 genes were identified as genes commonly induced by nicotine based on these two comparisons. Then relative gene expression was compared between α7nAChR+/+- and α7nAChR-/- -derived cells. 18 genes were finally selected whose expressions are suppressed (<1/2) in α7nAChR-/- -derived peritoneal macrophages. Conclusions: Our study represents the first detailed analysis focused on the new downstream signaling of α7nAChR in macrophages, generated by RNA-seq technology. We newly revealed the important anti-inflammatory role of Hes1 in the CAP using some functional experiments.

2018-09-01 | GSE103047 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of peritoneal macrophages Transcriptomes of Dnmt3a macrophage conditional knockout mouse

Project description:Purpose:The purpose of this study is to measure the gene expression profile in Dnmt3a conditional knockout macrophages. Methods:Dnmt3a conditional knockout macrophages mRNA profiles were generated by deep sequencing,using Illumina. Results: We mapped about 20 million sequence reads per sample to the mouse genome, identified hundreds of genes with significant mRNA variation during Dnmt3a conditional knockout in macrophages. Dnmt3a conditional knockout mRNA profiles were generated by deep sequencing

2016-05-30 | E-GEOD-74750 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of Vehicle or R-2-HG Treating Mouse Peritoneal Macrophages Transcriptomes

Project description:Purpose: The goals of this study are to screen differentially expressed genes in mouse peritoneal macrophages treated by vehicle or R-2-HG and to explore potential mechanisms of how R-2-HG regulating the process of macrophage activation. Methods: After RNA extraction, purification, and library construction, the samples were paired-end (PE) sequenced by Next-Generation Sequencing using an Illumina sequencing platform (Illumina HiSeq 2500). After sequencing, the filtered high-quality sequences (Clean Data) filtered from the original raw data were mapped to the Mus_musculus GRCm38.p4 (mm10) genome. Based on the mapped results, the expression level of each gene was calculated, and the samples of the different groups were subjected to further analysis for differences in expression, enrichment, and cluster analysis. Results: The mRNA expression levels of only a few genes were changed after R-2-HG treatment in mouse peritoneal macrophages, but HIF1A was not included. Conclusions:Regulating the macrophage activation by R-2-HG may not be due to its effect on gene transcription, and R-2-HG doses not affect the mRNA expression of HIF1A.

2024-07-31 | GSE181340 | GEO

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

| PRJNA867562 | ENA

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