Bulk RNA sequencing for classically activated macrophages (CAMs) from Ninj1+/+ and Ninj1-/- mice
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE155086 | GEO | 2020/09/04
REPOSITORIES: GEO
Similar Datasets
Project description:We have applied bulk RNA sequencing as an unbiased transcriptomics to demonstrate the mechanism underlying actions of sNinj1 in macrophage inflammation. The anti-inflammatory role of Ninj1 was verified by treating macrophages with the peptide Ninj11-56 (ML56), which mimic the soluble form of Ninj1 (sNinj1).
2020-09-04 | GSE154693 | GEO
Project description:Complex interplay between T helper (Th) cells and macrophages contributes to the formation and progression of atherosclerotic plaques. While Th1 cytokines promote inflammatory activation of lesion macrophages, Th2 cytokines attenuate macrophage-mediated inflammation and enhance their repair functions. In spite of its biologic importance, the biochemical and molecular basis of how Th2 cytokines promote maturation of anti-inflammatory macrophages is not understood. We show here that in response to interleukin-4 (IL-4), signal transducer and activator of transcription 6 (STAT6) and PPARg-coactivator-1b (PGC-1b) induce macrophage programs for fatty acid oxidation and mitochondrial biogenesis. Transgenic expression of PGC-1b primes macrophages for alternative activation and strongly inhibits proinflammatory cytokine production, whereas inhibition of oxidative metabolism or RNAi-mediated knockdown of PGC-1b attenuates this immune response. These data elucidate a molecular pathway that directly links mitochondrial oxidative metabolism to the anti-inflammatory program of macrophage activation, suggesting a potential role for metabolic therapies in treating atherogenic inflammation. Total RNA was prepared from three independent experimental replicates using Trizol reagent (Invitrogen) and validated by northern blot. Microarray experiments were performed with 20-25 ?g of total RNA, which was labelled with fluorescent nucleotides and hybridized to murine cDNA slides. Hybridized slides were interrogated via an Agilent scanner. Cells were activated with either interleukin-4, interferon-gamma/lipo-polysaccharide, or vehicle in low-glucose media.
2006-09-15 | E-SMDB-3728 | biostudies-arrayexpress
Project description:Cellular interactions are critical during development, tissue fitness and epithelial tumor development. The expression levels of specific genes confer to tumoral cells a survival advantage versus the normal neighboring cells. As a consequence, cells surrounding tumors are eliminated and engulfed by macrophages. We propose a novel scenario in which circulating cells facing a tumor can reproduce these cellular interactions. In vitro cultured macrophages from murine bone marrow were used to investigate this hypothesis. M1 macrophages in tumoral medium upregulated markers of a suboptimal condition, such as Sparc and TyrRS, and undergo apoptosis. However, M2 macrophages display higher Myc expression levels and proliferate at the expense of M1. Resulting M1 apoptotic debris is engulfed by M2 in a Sparc- and TyrRS-dependent manner. These findings suggest that tumor-dependent macrophage elimination could deplete immune response against tumors. This possibility could be relevant for macrophage based anti-tumoral strategies.
| S-EPMC5769648 | biostudies-literature
Project description:Using RNA-seq, we have reported that signaling crosstalk among IFN-γ and LPS is integrated at the level of transcriptome and have associated with TFs and TcoFs changes. In addition, we also argue that the transcriptional differences between BMDMs and RAW264.7 macrophage cell line as well as IL-4 and IL-13 on M2 macrophages activation.
2018-01-23 | GSE103958 | GEO
Project description:Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived human M1- and M2-like macrophage profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to establish a high resolution transcriptome of human macrophages. Total RNA was isolated from classically and aternative activated human macrophages.mRNA profiles were generated by deep sequencing og M1 and M2 macrophages from 3 donors using Illumina HiSeqSQ. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Casava1.8 and TopHat followed by Cufflinks. qRT–PCR validation was performed using LightCycler and SYBR Green assays. mRNA profiles were generated by deep sequencing og M1 and M2 macrophages from 3 donors using Illumina HiSeqSQ.
2012-10-01 | E-GEOD-36952 | biostudies-arrayexpress
Project description:To determine the transcriptional profile associated with macrophage polarization to M1 or M2, we cultured macrophages derived from monocytes for 7 days and treated them with IFNg, IL-4, TNF, LPS, and LPS+IFNg (n=7). Psoriasis lesional and non-lesional skin biopsies were included (n=5 pairs).
2010-03-01 | GSE18686 | GEO
Project description:Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived human M1- and M2-like macrophage profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to establish a high resolution transcriptome of human macrophages. Total RNA was isolated from classically and aternative activated human macrophages.mRNA profiles were generated by deep sequencing og M1 and M2 macrophages from 3 donors using Illumina HiSeqSQ. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Casava1.8 and TopHat followed by Cufflinks. qRT–PCR validation was performed using LightCycler and SYBR Green assays.
2012-10-01 | GSE36952 | GEO
Project description:The purpose of this study is to identify novel markers for the type II activated macrophage, which is generated by classical stimulation in the presence if IgG immune complexes. These cells gererally produce high levels of IL-10 and low levels of IL-12, in comparison to classically activated macrophages. We wish to identify gene expression which is enriched in Type II activated macrophages in comparison to classically activated macrophages. Keywords: Stimulation comparison
2006-05-17 | GSE4811 | GEO
Project description:The purpose of this study is to identify novel markers for the type II activated macrophage, which is generated by classical stimulation in the presence if IgG immune complexes. These cells gererally produce high levels of IL-10 and low levels of IL-12, in comparison to classically activated macrophages. We wish to identify gene expression which is enriched in Type II activated macrophages in comparison to classically activated macrophages. Experiment Overall Design: The design of this experiment is to simulateously stimulate two popultions of macrophages and compare their gene expression. In this case, macrophages are primed overnight with IFN-gamma, washed, then stimulated with LPS (Classically) or LPS+Immune complexes (Type II).
2008-06-13 | E-GEOD-4811 | biostudies-arrayexpress
Project description:Macrophages are important cells of the innate immune system, and their study is essential to gain greater understanding of the inflammatory nature of psoriasis. We used immunohistochemistry and double-label immunofluorescence to characterize CD163(+) macrophages in psoriasis. Dermal macrophages were increased in psoriasis compared with normal skin and were identified by CD163, RFD7, CD68, lysosomal-associated membrane protein 2 (LAMP2), stabilin-1, and macrophage receptor with collagenous structure (MARCO). CD163(+) macrophages expressed C-lectins CD206/macrophage mannose receptor and CD209/DC-SIGN, as well as costimulatory molecules CD86 and CD40. They did not express mature dendritic cell (DC) markers CD208/DC-lysosomal-associated membrane glycoprotein, CD205/DEC205, or CD83. Microarray analysis of in vitro-derived macrophages treated with IFN-? showed that many of the genes upregulated in macrophages were found in psoriasis, including STAT1, CXCL9, Mx1, and HLA-DR. CD163(+) macrophages produced inflammatory molecules IL-23p19 and IL-12/23p40 as well as tumor necrosis factor (TNF) and inducible nitric oxide synthase (iNOS). These data show that CD163 is a superior marker of macrophages, and identifies a subpopulation of "classically activated" macrophages in psoriasis. We conclude that macrophages are likely to contribute to the pathogenic inflammation in psoriasis, a prototypical T helper 1 (Th1) and Th17 disease, by releasing key inflammatory products.
| S-EPMC2939947 | biostudies-literature