{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"contact_person":["Menno P.J. de Winther"],"full_dataset_link":["https://ega-archive.org/dacs/EGAC00001001123"],"host":["EGA"],"description":["EGA DAC EGAC00001001123"],"repository":["EGA"],"email":["m.dewinther@amc.uva.nl"],"pubmed_abstract":["Macrophages are heterogeneous leukocytes regulated in a tissue- and disease-specific context. While <i>in vitro</i> macrophage models have been used to study diseases empirically, a systematic analysis of the transcriptome thereof is lacking. Here, we acquired gene expression data from eight commonly-used <i>in vitro</i> macrophage models to perform a meta-analysis. Specifically, we obtained gene expression data from unstimulated macrophages (M0) and macrophages stimulated with lipopolysaccharides (LPS) for 2-4 h (M-LPS<sub>early</sub>), LPS for 24 h (M-LPS<sub>late</sub>), LPS and interferon-γ (M-LPS+IFNγ), IFNγ (M-IFNγ), interleukin-4 (M-IL4), interleukin-10 (M-IL10), and dexamethasone (M-dex). Our meta-analysis identified consistently differentially expressed genes that have been implicated in inflammatory and metabolic processes. In addition, we built macIDR, a robust classifier capable of distinguishing macrophage activation states with high accuracy (>0.95). We classified <i>in vivo</i> macrophages with macIDR to define their tissue- and disease-specific characteristics. We demonstrate that alveolar macrophages display high resemblance to IL10 activation, but show a drop in IFNγ signature in chronic obstructive pulmonary disease patients. Adipose tissue-derived macrophages were classified as unstimulated macrophages, but acquired LPS-activation features in diabetic-obese patients. Rheumatoid arthritis synovial macrophages exhibit characteristics of IL10- or IFNγ-stimulation. Altogether, we defined consensus transcriptional profiles for the eight <i>in vitro</i> macrophage activation states, built a classification model, and demonstrated the utility of the latter for <i>in vivo</i> macrophages."],"pubmed_title":["Meta-Analysis of <i>in vitro</i>-Differentiated Macrophages Identifies Transcriptomic Signatures That Classify Disease Macrophages <i>in vivo</i>."],"pubmed_authors":["Chen Hung-Jen HJ, Li Yim Andrew Y F AYF, Griffith Guillermo R GR, de Jonge Wouter J WJ, Mannens Marcel M A M MMAM, Ferrero Enrico E, Henneman Peter P, de Winther Menno P J MPJ"],"additional_accession":[]},"is_claimable":false,"name":"AMC Macrophage Data Access Committee","description":"Data Access Committee EGAC00001001123","dates":{"output":"2025-1-9"},"accession":"EGAC00001001123","cross_references":{"TAXONOMY":["9606"],"pubmed":["31921150"],"EGA":["EGAS00001003451","EGAD00001004584"]}}