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Small RNA-sequencing in apoptotic macrophages

ABSTRACT: Small RNA-sequencing in apoptotic macrophages

PROVIDER: PRJNA269106 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1691010.fastq.gz	Fastqsanger.gz
	SRR1691011.fastq.gz	Fastqsanger.gz
	SRR1691012.fastq.gz	Fastqsanger.gz
	SRR1691013.fastq.gz	Fastqsanger.gz
	SRR1691014.fastq.gz	Fastqsanger.gz

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High-throughput small RNA sequencing of human primary macrophages stimulated with staurosporine

Project description:Analysis of small RNAs that are deregulated in apoptotic macrophages

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Apoptotic cells induce proliferation of peritoneal macrophages

Project description:The interaction of macrophages with apoptotic cells is required for efficient resolution of inflammation. While apoptotic cell removal prevents inflammation due to secondary necrosis, it also alters the macrophage phenotype to hinder further inflammatory reactions. The interaction between apoptotic cells and macrophages is often studied by chemical or biological induction of apoptosis, which may introduce artifacts by affecting the macrophages as well and/or triggering unrelated signaling pathways. Here, we set up a pure cell death system in which NIH 3T3 cells expressing dimerizable Caspase-8 were co-cultured with peritoneal macrophages in a transwell system. Phenotype changes in macrophages induced by apoptotic cells were evaluated by RNA sequencing, which revealed an unexpectedly dominant impact on macrophage proliferation. This was confirmed in functional assays with primary peritoneal macrophages and IC-21 macrophages. Moreover, inhibition of apoptosis during Zymosan-induced peritonitis in mice decreased mRNA levels of cell cycle mediators in peritoneal macrophages. Proliferation of macrophages in response to apoptotic cells may be important to increase macrophage numbers to allow efficient clearance and resolution of inflammation.

2021-03-18 | GSE164709 | GEO

High-throughput small RNA sequencing of mouse primary macrophages treated with M-CSF withdrawal

Project description:Analysis of small RNAs that are deregulated in apoptotic macrophages

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small RNAnext Generation Sequencing of bone marrow-derived macrophages treated in M-CSF withdrawal medium

Project description:The goal of this study is to investigate the presence of novel small RNAs in apoptotic macrophage Method: cultured mouse (bl6 line) bone marrow were differentiated in for 7 days in conditioned medium, in preence of Macrophage-Colony Stimulating Factor (M-CSF). M-CSF also stimulates the survive of macrophages by activating PI3K/AKT pathway. In accordance to previous publication (Lombardo, E., Alvarez-Barrientos, A., Maroto, B., Bosca, L., and Knaus, U.G, 2007, TLR4-mediated survival of macrophages is MyD88 dependent and requires TNF-alpha autocrine signalling, J Immunol 178, 3731-3739) apoptosis was induced in culturaed bone marrow-derived macrophages upon 36 hr of M-CSF withdrawal. Total RNA was isolated and a small RNA library was made using "Small RNA sequencing kit" (Illumina), according to the manufacturer’s instructions.

2015-09-16 | E-GEOD-47408 | biostudies-arrayexpress

Small non-coding RNA sequencing of human monocyte-derived macrophages

Project description:The goal of this experiment was to identify the differential expression of microRNAs in human polarised macrophages. We used monocyte-derived macrophages isolated from 8 different healthy invididuals. Differentiated macrophages were polarised towards the pro-inflammatory M1-like phenotype, by using LPS and INF- . Total RNA was extracted and sent for small-RNA sequencing to the company Novogene.

2021-12-01 | GSE152371 | GEO

Apoptotic cells induce proliferation of peritoneal macrophages

Project description:Apoptotic cells induce proliferation of peritoneal macrophages

| PRJNA691612 | ENA

Small non-coding RNA sequencing of human monocyte-derived macrophages

Project description:Small non-coding RNA sequencing of human monocyte-derived macrophages

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The identity of the apoptotic cell explains the functional diversity of the efferocytic macrophages

Project description:Macrophages are a functionally heterogeneous cell population, critical for the clearance of apoptotic cells. Apoptotic cells have so far been regarded as cells with homogeneous characteristics, often neglecting their original cell lineage identity. Contrary to this, we have observed that the identities of apoptotic cells matter, since they diversify the profile of efferocytic macrophages in vitro and in mouse models of tissue damage. Apoptotic neutrophils trigger a tissue remodeling macrophage signature, while T cells and hepatocytes respectively do not change or promote a tolerogenic macrophage response. Accordingly, the in vivo transfer of macrophages fed with apoptotic neutrophils, but not the transfer of macrophages fed with other apoptotic cells, promotes tissue remodeling. Finally, using a mouse model of parasite-induced tissue pathology, we found that the presence of specific apoptotic cells while simultaneously engaging select phagocytic receptors, i.e. AXL and MERTK by apoptotic neutrophils, diversifies macrophage function. These data reveal that the identity of an apoptotic cell should not be neglected since it drives macrophage transcriptomic and functional heterogeneity.

2024-02-16 | E-MTAB-13780 | biostudies-arrayexpress

The identity of the apoptotic cell explains the functional diversity of the efferocytic macrophages

2024-02-16 | E-MTAB-13753 | biostudies-arrayexpress

WT and Ccr2-/- small intestinal macrophages

Project description:To better determine heterogeneity of small intestinal macrophages, CD64+ macrophages were sorted for single cell RNA sequencing

2023-08-18 | GSE234018 | GEO

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