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Oxidative metabolism and PGC-1 attenuate macrophage-mediated inflammation

ABSTRACT: 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. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

ORGANISM(S): Mus musculus

PROVIDER: GSE5003 | GEO | 2006/06/07

SECONDARY ACCESSION(S): PRJNA95787

REPOSITORIES: GEO

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Oxidative metabolism and PGC-1 attenuate macrophage-mediated inflammation

Project description: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. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Complex

2010-07-01 | E-GEOD-5003 | biostudies-arrayexpress

Gene expression change caused by CYS4 alleles

Project description:Each strain was grown overnight then diluted in fresh YPD to 10% v/v and grown for 3 hours at 30'C. Total RNA was isolated using an RNeasy mini kit, reverse transcribed, labeled with either Cy3 or Cy5, and hybridized to epoxy-coated slides with 6388, 70mer oligos (Qiagen-Operon). After an overnight hybridization, microarrays were scanned using a ScanArray Express laser scanner.

2008-12-30 | GSE14102 | GEO

circRNA Microarray for human colorectal adenocarcinoma and normal mucosa

Project description:Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols. Briefly, total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing random primer according to Arraystar’s Super RNA Labeling protocol (Arraystar Inc.). The labeled cRNAs were hybridized onto the Arraystar Human circRNA Array (8x15K, Arraystar). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

2020-02-05 | GSE138589 | GEO

HSF1 Mouse Fibroblast Heat Shock - Scanner7

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2005-08-05 | GSE3074 | GEO

HTC avian macrophage cells stimulated with 3 species of Eimeria across a 48 hour timecourse

Project description:HTC avain macrophage cell line was stimulated with E. tenella, acervulina, and maxima for 0, 4, 18, and 48 hours. Total RNA was extracted, mRNA was purified, and RNA samples were directly labeled with Alexa555 or 647. The experiment was performed in loop format, so that each sample was labeled with both dyes and hybridized to two different slides. Images were acquired by the Applied Precision ArrayWoRx scanner and software and then intensity values were obtained using Softworx Tracker. Keywords: timecurse, species comparison

2005-12-06 | GSE3723 | GEO

Arraystar m6A-mRNA&lncRNA Epitranscriptomic Microarray Service for 6 Mouse samples

Project description:Total RNA from each sample was quantified using the NanoDrop ND-1000 and RNA integrity was assessed by Bioanalyzer 2100 or Mops electrophoresis. The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols. Briefly, the total RNAs were immunoprecipitated with anti-N6-methyladenosine (m6A) antibody. The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”. The “IP” and “Sup” RNAs were labeled with Cy5 and Cy3 respectively as cRNAs in separate reactions using Arraystar RNA Labeling protocol. The cRNAs were combined together and hybridized onto Arraystar Mouse mRNA&lncRNA Epitranscriptomic Microarray (8x60K, Arraystar). After washing the slides, the arrays were scanned in two-color channels by an Agilent Scanner G2505C.Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. After Spike-in normalization, the probe signals having Present (P) or Marginal (M) QC flags in a certain proportion were retained for further “m6A quantity” analyses. “m6A quantity” was calculated for the m6A methylation amount based on the IP (Cy5-labelled) normalized intensities. Differentially m6A-methylated RNAs between two comparison groups were identified by filtering with the fold change and statistical significance (p-value) thresholds. Hierarchical Clustering was performed to show the distinguishable m6A-methylation pattern among samples.

2022-11-24 | GSE218412 | GEO

A distinct and unique M2 transcriptional program expressed by tumor-associated macrophages

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2005-02-18 | GSE2279 | GEO

Transcription profiling of classically activated, alternatively activated, and naive mouse macrophages

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

Microarray analysis reveals potential circRNA biomarkers in human acral lentiginous melanoma

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2024-06-26 | GSE270439 | GEO

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