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High-throughput sequencing analysis of mouse FABP5 KO BMDM cell transcriptomes with overexpression of FABP5 WT or FABP5 C127S after LPS treatment

ABSTRACT: High-throughput sequencing analysis of mouse FABP5 KO BMDM cell transcriptomes with overexpression of FABP5 WT or FABP5 C127S after LPS treatment

PROVIDER: PRJNA755440 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15494853_1.fastq.gz	Fastqsanger.gz
	SRR15494853_2.fastq.gz	Fastqsanger.gz
	SRR15494854_1.fastq.gz	Fastqsanger.gz
	SRR15494854_2.fastq.gz	Fastqsanger.gz
	SRR15494855_1.fastq.gz	Fastqsanger.gz

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High-throughput sequencing analysis of mouse FABP5 KO BMDM cell transcriptomes with overexpression of FABP5 WT or FABP5 C127S after LPS treatment

Project description:Purpose: Mouse BMDM is the universal cell type of studying innate immunity. This study was designed to analyze LPS induced innate immune response and the gene expression in FABP5 KO BMDMs with overexpression of FABP5 WT or FABP5 C127S. Methods: FABP5 KO BMDMs were nucleofected with 5 μg pXJ40-3xFlag-FABP5 WT or C127S plasmid using the Amaxa Mouse Macrophage Nucleofector Kit (Lonza, VPA-1009) following the manufacturer’s instructions. Replace medium 6 hours post Nucleofection and add 500 ng/mL LPS to the fresh medium. 24 hours after treatment, harvest cells by using GenElute Single Cell RNA Purification Kit (Sigma, RNB300) and perform RNA-seq. Then mRNA profiles of these samples were generated by high-throughput sequencing analysis, using Illumina NovaSeq6000. And the differential mRNA profiles were analyzed. Results: mRNA profiles were analyzed, and differential expression profiles were compared. Conclusions: Our study demonstrated the transcriptional profiles of FABP5 KO BMDMs with overexpression of FABP5 WT or FABP5 C127S upon LPS treatment, with biologic replicates, generated by RNA-seq technology.

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High-throughput sequencing Analysis of mouse BMDM cell Transcriptomes after LPS Challenge

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2021-08-06 | GSE155801 | GEO

High-throughput sequencing Analysis of mouse BMDM cell Transcriptomes

Project description:Purpose: Mouse BMDM is the universal cell type of studying innate immunity.This study was to analyze LPS induced innate immune respone and the relationship between serine synthesis pathway and LPS induced innate immune respone Methods: BMDM cells were treated with or without LPS for 6 hours in the pressence of phgdh inhibitor or not. Then mRNA profiles of these samles were generated by High-throughput sequencing analysis, in triplicate, using illumina HiSeqTM 2000. And the differencial mRNA profiles were analyzed. Results: mRNA profiles about 23002 genes were analyzed, and differencial expression profiles were compared . Conclusions: Our study represents the first detailed analysis of transcriptomes of mouse BMDM treated with LPS and phgdh inhibitor, with biologic replicates, generated by RNA-seq technology. This data was useful to analyze the relationship between serine synthesis pathway and LPS induced innate immune respone

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High-throughput sequencing Transcriptomes Analysis of WT and Kcnj2 KO mouse BMDMs treated with LPS or kir2.1 inhibitor

Project description:Purpose:Mouse BMDM is the universal cell type of studying innate immunity.This study was to analyze LPS induced innate immune response and the relationship between the inward rectifier potassium channel Kir2.1 and LPS induced innate immune respone Methods: WT and Kcnj2 KO BMDM cells were treated with or without LPS for 6 hours in the presence of kir2.1 inhibitor ML133 or not. Then mRNA profiles of these samles were generated by High-throughput sequencing analysis, in triplicate, using illumina HiSeq 2000. And the differential mRNA profiles were analyzed. Results: mRNA profiles of more than 20000 genes were analyzed, and differential expression profiles were compared . Conclusions: Our study represents the first detailed analysis of transcriptomes of WT and Kcnj2 KO mouse BMDM treated with LPS or kir2.1 inhibitor, with biologic replicates, generated by RNA-seq technology. This data was useful to analyze the relationship between Kir2.1 and LPS induced innate immune respone

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Project description:Purpose:Mouse BMDM is the universal cell type of studying innate immunity.This study was to analyze LPS induced innate immune respone and the relationship between the membrane potential and LPS induced innate immune respone Methods: WT BMDM cells were treated with or without LPS for 6 hours in the pressence of membranepotential depolarization stimuli. Then mRNA profiles of these samles were generated by High-throughput sequencing analysis, in triplicate, using Illumina HiSeq /Novaseq or MGI2000. And the differencial mRNA profiles were analyzed. Results: mRNA profiles of more than 20000 genes were analyzed, and differencial expression profiles were compared . Conclusions: Our study represents the first detailed analysis of transcriptomes of WT and membrane potential depolarized macrophages, with biologic replicates, generated by RNA-seq technology. This data was useful to analyze the relationship between membrane potential and LPS induced innate immune respone

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Expression data from pig BMDM treated with salmonella LPS

Project description:Mouse bone marrow-derived macrophages (BMDM) grown in macrophage colony-stimulating factor (CSF-1) have been used widely in studies of macrophage biology and the response to toll-like receptor agonists. We investigated whether similar cells could be derived from the domestic pig. Cultivation of pig bone marrow cells for 5-7 days in presence of rhCSF-1 generated a pure population of BMDM that expressed the usual macrophage markers (CD14, CD16, CD163, CD172a), are potent phagocytic cells and produced tumor necrosis factor (TNF) in response to lipopolysaccharide (LPS). Bone marrow cells could be stored frozen and thawed, providing a renewable resource. We profiled gene expression in pig BMDM from outbred animals (Large-White Landrace F1cross) responding to LPS using Affymetrix microarrays. The temporal cascade of inducible and repressible genes more closely-resembled human than mouse macrophages, and included genes involved in tryptophan metabolism (IDO, KYN), lymphoattractant chemokines (CCL20) and the vitamin D3-converting enzyme Cyp27B1. Conversely, pig BMDM, like human macrophages, did not induce genes involved in arginine metabolism, nor did they produce nitric oxide. The data establish pig BMDM as an alternative tractable model for the study of macrophage transcriptional control. RNA for gene expression analysis was collected at time points 0, 2, 7 and 24 hours post LPS stimulation (100ng/ml). Each time point included BMDM from the same three pigs and each cell culture was replicated. The replicate of the pig3_24h was not suitable for RNA analysis. Therefore, a total of 23 microarrays were hybridized.

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High-throughput sequencing Analysis of mouse BMDM cell Transcriptomes after LPS Challenge

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Expression data from pig BMDM treated with salmonella LPS

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