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Bulk RNA-seq of foamy and non-foamy intimal macrophages from ApoE -/- mouse

ABSTRACT: Bulk RNA-seq of foamy and non-foamy intimal macrophages from ApoE -/- mouse

PROVIDER: PRJNA477844 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7425020.fastq.gz	Fastqsanger.gz
	SRR7425021.fastq.gz	Fastqsanger.gz
	SRR7425022.fastq.gz	Fastqsanger.gz
	SRR7425017.fastq.gz	Fastqsanger.gz
	SRR7425018.fastq.gz	Fastqsanger.gz

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Bulk RNA-seq of foamy and non-foamy intimal macrophages from ApoE -/- mouse

Project description:Macrophages in atherosclerotic aorta are major population in lesion and contributes to lesion formation by becoming foam cells. To investigate in vivo transcriptome profiles of those macrophages, we extracted foamy and non-foamy macrophages from atherosclerotic aorta using lipid probe-based flow cytometry sorting. Our data indicates that intima non-foamy and foamy macrophages show different mRNA expressions. Rather than non-foamy macrophages, foamy macrophages expressed more genes related to cholesterol metabolism, oxidative phosphorylation, lysosome and so on. The non-foamy macrophages expressed more genes related to immune response (Il-1b related pathways, TNF, TLR signaling pathways) than foamy macrophages.

2018-08-30 | GSE116239 | GEO

Genomic profile of foamy and non-foamy granuloma macrophages from fat-fed ApoE null mice or control mice fed a normal diet

Project description:Formation of foam cell macrophages (FCMs), which sequester extracellular modified lipids, is a key event in atherosclerosis. How lipid loading affects macrophage phenotype is controversial, with evidence suggesting either pro- or anti-inflammatory consequences. To investigate this further, we compared the transcriptomes of foamy and non-foamy macrophages (NFMs) that accumulate in the subcutaneous granulomas of fed-fat ApoE null mice and normal chow fed wild-type mice in vivo. Consistent with previous studies, LXR/RXR pathway genes were significantly over-represented among the genes up-regulated in foam cell macrophages. Unexpectedly, the hepatic fibrosis pathway, associated with platelet derived growth factor and transforming growth factor-? action, was also over-represented. Several collagen polypeptides and proteoglycan core proteins as well as connective tissue growth factor and fibrosis-related FOS and JUN transcription factors were up-regulated in foam cell macrophages. Increased expression of several of these genes was confirmed at the protein level in foam cell macrophages from subcutaneous granulomas and in atherosclerotic plaques. Moreover, phosphorylation and nuclear translocation of SMAD2, which is downstream of several transforming growth factor-? family members, was also detected in foam cell macrophages. We conclude that foam cell formation in vivo leads to a pro-fibrotic macrophage phenotype, which could contribute to plaque stability, especially in early lesions that have few vascular smooth muscle cells. Samples (n=4/group): Foam cell macrophages (FCM) isolated from inflammatory sponges placed in ApoE null mice fed a high-fat diet (n=4), non-foamy macrophages (NFM) isolated from inflammatory sponges placed in control mice fed a normal diet (n=4).

2015-07-23 | E-GEOD-70126 | biostudies-arrayexpress

Bulk RNA-seq of aorta intima resident macrophage from B6, and adventitia macrophages from ApoE-/- mice

Project description:Macrophages in atherosclerotic aorta are major population in lesion and contributes to lesion formation by becoming foam cells. To investigate in determine diversity of arterial macrophage, we extracted aorta intima resident macrophages (CD11c+ MHC II+ CD64+ macrophages from C57BL/6 mice, as well as adventitia macrophages from atherosclerotic aorta (which complement our prior submissions of foamy and non-foamy intima macrophage). Our data identify unique gene expression signatures for these different macrophage populations in the aorta.

2020-07-23 | GSE154921 | GEO

Genomic profile of foamy and non-foamy granuloma macrophages from fat-fed ApoE null mice or control mice fed a normal diet

Project description:Formation of foam cell macrophages (FCMs), which sequester extracellular modified lipids, is a key event in atherosclerosis. How lipid loading affects macrophage phenotype is controversial, with evidence suggesting either pro- or anti-inflammatory consequences. To investigate this further, we compared the transcriptomes of foamy and non-foamy macrophages (NFMs) that accumulate in the subcutaneous granulomas of fed-fat ApoE null mice and normal chow fed wild-type mice in vivo. Consistent with previous studies, LXR/RXR pathway genes were significantly over-represented among the genes up-regulated in foam cell macrophages. Unexpectedly, the hepatic fibrosis pathway, associated with platelet derived growth factor and transforming growth factor-β action, was also over-represented. Several collagen polypeptides and proteoglycan core proteins as well as connective tissue growth factor and fibrosis-related FOS and JUN transcription factors were up-regulated in foam cell macrophages. Increased expression of several of these genes was confirmed at the protein level in foam cell macrophages from subcutaneous granulomas and in atherosclerotic plaques. Moreover, phosphorylation and nuclear translocation of SMAD2, which is downstream of several transforming growth factor-β family members, was also detected in foam cell macrophages. We conclude that foam cell formation in vivo leads to a pro-fibrotic macrophage phenotype, which could contribute to plaque stability, especially in early lesions that have few vascular smooth muscle cells.

2015-07-23 | GSE70126 | GEO

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Project description:Aortic macrophages and endothelial cells of apoE KO mice were sorted and analyzed by microarray 2 weeks after regression was induced by adenoviral transfer of apoE. Aortic macrophages (CD45+ F4/80+ CD11b+) and endothelial cells (CD45- CD31+) were sorted from apoE KO mice and the RNA extracted and hybridized to Affymetrix Mouse Gene 1.0 ST array. We pooled aortas from 5 mice for each sort.

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Aortic macrophages and endothelial cells of apoE KO mice aortas after plaque regression induced apoE adenoviral transfer

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Bulk RNA sequencing of Cd45+ cells from brains of aged Alzheimer's mice bearing human APOE knockin

Project description:Here we perform bulk RNA sequencing of immune cells of aged AD mice bearing knock-in of human APOE variants in the murine APOE locus.

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Single-cell RNA-sequencing of adventitial and medial/intimal cells in 8-12-week-old wildtype and ApoE-/- mice

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Bulk RNA-seq of aorta intima resident macrophage from B6, and adventitia macrophages from ApoE-/- mice

Project description:Bulk RNA-seq of aorta intima resident macrophage from B6, and adventitia macrophages from ApoE-/- mice

| PRJNA647885 | ENA

Transcriptome Data of Peritoneal Macrophages Isolated from ApoE-/-/Ch25h-/- Mice

Project description:Cholesterol 25-hydroxylase (Ch25h) has been previously demonstrated to be required for anti-inflammatory effect and anti-viral activity, while also promoting foam cell formation. In order to delineate the role of Ch25h in atherosclerosis, we isolated peritoneal macrophages (PMs) from mice lacking ApoE and Ch25h (i.e., ApoE-/-/Ch25h-/-) compared to their wildtype littermates (i.e., ApoE-/-/Ch25h+/+) for transcriptome analysis, in biological duplicates (n=12 pooled mice per group). Deep-sequencing analysis revealed that PMs ablated with Ch25h were prone to the pro-inflammatory M1 phenotype as well as increased cholesterol biosynthesis. Overall, we found that Ch25h is integral to atheroprotection through the preservation of M2 polarization and suppression of intracelllular cholesterol content.

2017-10-05 | GSE90983 | GEO

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