[1]
Murray PJ, Allen JE, Biswas SK, et al. Macrophage activation and polarization: nomenclature and experimental guidelines. Immunity 2014; 41(1): 14-20.
[2]
Zhao S, Fung-Leung WP, Bittner A, Ngo K, Liu X. Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells. PLoS One 2014; 9(1)e78644
[3]
Haase T, Börnigen D, Müller C, Zeller T. Systems medicine as an emerging tool for cardiovascular genetics. Front Cardiovasc Med 2016; 3: 27.
[4]
Xu S. Transcriptome profiling in systems vascular medicine. Front Pharmacol 2017; 8: 563.
[5]
Hrdlickova R, Toloue M, Tian B. RNA-Seq methods for transcriptome analysis. Wiley Interdiscip Rev RNA 2017; 8(1): 10.
[6]
Hume DA, Freeman TC. Transcriptomic analysis of mononuclear phagocyte differentiation and activation. Immunol Rev 2014; 262(1): 74-84.
[7]
Derlindati E, Dei Cas A, Montanini B, et al. Transcriptomic analysis of human polarized macrophages: more than one role of alternative activation? PLoS One 2015; 10(3)e0119751
[8]
Becker M, De Bastiani MA, Parisi MM, et al. Integrated transcriptomics establish macrophage polarization signatures and have potential applications for clinical health and disease. Sci Rep 2015; 5: 13351.
[9]
Tugal D, Liao X, Jain MK. Transcriptional control of macrophage polarization. Arterioscler Thromb Vasc Biol 2013; 33(6): 1135-44.
[10]
Jablonski KA, Gaudet AD, Amici SA, Popovich PG, Guerau-de-Arellano M. Control of the inflammatory macrophage transcriptional signature by miR-155. PLoS One 2016; 11(7)e0159724
[11]
Graff JW, Dickson AM, Clay G, McCaffrey AP, Wilson ME. Identifying functional microRNAs in macrophages with polarized phenotypes. J Biol Chem 2012; 287(26): 21816-25.
[12]
Karo-Atar D, Itan M, Pasmanik-Chor M, Munitz A. MicroRNA profiling reveals opposing expression patterns for miR-511 in alternatively and classically activated macrophages. J Asthma 2015; 52(6): 545-53.
[13]
Czimmerer Z, Varga T, Kiss M, et al. The IL-4/STAT6 signaling axis establishes a conserved microRNA signature in human and mouse macrophages regulating cell survival via miR-342-3p. Genome Med 2016; 8(1): 63.
[14]
Zhang Y, Zhang Y, Li X, Zhang M, Lv K. Microarray analysis of circular RNA expression patterns in polarized macrophages. Int J Mol Med 2017; 39(2): 373-9.
[15]
Schmidt SV, Krebs W, Ulas T, et al. The transcriptional regulator network of human inflammatory macrophages is defined by open chromatin. Cell Res 2016; 26(2): 151-70.
[16]
Xue J, Schmidt SV, Sander J, et al. Transcriptome-based network analysis reveals a spectrum model of human macrophage activation. Immunity 2014; 40(2): 274-88.
[17]
Piccolo V, Curina A, Genua M, et al. Opposing macrophage polarization programs show extensive epigenomic and transcriptional cross-talk. Nat Immunol 2017; 18(5): 530-40.
[18]
Lurier EB, Dalton D, Dampier W, et al. Transcriptome analysis of IL-10-stimulated (M2c) macrophages by next-generation sequencing. Immunobiology 2017; 222(7): 847-56.
[19]
Lin J, Hu Y, Nunez S, et al. Transcriptome-Wide Analysis Reveals Modulation of Human Macrophage Inflammatory Phenotype Through Alternative Splicing. Arterioscler Thromb Vasc Biol 2016; 36(7): 1434-47.
[20]
de Bruin RG, Shiue L, Prins J, et al. Quaking promotes monocyte differentiation into pro-atherogenic macrophages by controlling pre-mRNA splicing and gene expression. Nat Commun 2016; 7: 10846.
[21]
Das A, Yang CS, Arifuzzaman S, et al. High-resolution mapping and dynamics of the transcriptome, transcription factors, and transcription co-factor networks in classically and alternatively activated macrophages. Front Immunol 2018; 9: 22.
[22]
Wynn TA, Chawla A, Pollard JW. Macrophage biology in development, homeostasis and disease. Nature 2013; 496(7446): 445-55.
[23]
Nikiforov N, Galstyan K, Nedosugova L, Elizova N, Kolmychkova K, Ivanova E. Proinflammatory monocyte polarization in type 2 diabetes mellitus and coronary heart disease. Vessel Plus 2017; 1: 192-5.
[24]
Miao X, Leng X, Zhang Q. The current state of nanoparticle-induced macrophage polarization and reprogramming research. Int J Mol Sci 2017; 18(2): 336.
[25]
Lavin Y, Mortha A, Rahman A, Merad M. Regulation of macrophage development and function in peripheral tissues. Nat Rev Immunol 2015; 15(12): 731-44.
[26]
de Franciscis S, Metzinger L, Serra R. The discovery of novel genomic, transcriptomic, and proteomic biomarkers in cardiovascular and peripheral vascular disease: The state of the art. BioMed Res Int 2016; 20167829174
[27]
Geeraerts X, Bolli E, Fendt SM, Van Ginderachter JA. Macrophage metabolism as therapeutic target for cancer, atherosclerosis, and obesity. Front Immunol 2017; 8: 289.
[28]
Itoh M, Kojima M, Nagao-Sato S, et al. Automated workflow for preparation of cDNA for cap analysis of gene expression on a single molecule sequencer. PLoS One 2012; 7(1)e30809
[29]
Noguchi S, Arakawa T, Fukuda S, et al. FANTOM5 CAGE profiles of human and mouse samples. Sci Data 2017; 4170112
[30]
Baillie JK, Arner E, Daub C, et al. Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease. PLoS Genet 2017; 13(3)e1006641
[31]
Denisenko E, Guler R, Mhlanga MM, Suzuki H, Brombacher F, Schmeier S. Genome-wide profiling of transcribed enhancers during macrophage activation. Epigenetics Chromatin 2017; 10(1): 50.
[32]
Bronte V, Murray PJ. Understanding local macrophage phenotypes in disease: modulating macrophage function to treat cancer. Nat Med 2015; 21(2): 117-9.
[33]
Attri KS, Mehla K, Shukla SK, Singh PK. Microscale Gene Expression Analysis of Tumor-Associated Macrophages. Sci Rep 2018; 8(1): 2408.
[34]
Buscher K, Ehinger E, Gupta P, et al. Natural variation of macrophage activation as disease-relevant phenotype predictive of inflammation and cancer survival. Nat Commun 2017; 8: 16041.
[35]
Lin Z, Changfu H, Fengling Z, et al. Long non-coding RNA deep sequencing reveals the role of macrophage in liver disorders. Oncotarget 2017; 8(70): 114966-79.
[36]
Zhang H, Xue C, Wang Y, et al. Deep RNA sequencing uncovers a repertoire of human macrophage long intergenic noncoding RNAs modulated by macrophage activation and associated with cardiometabolic diseases. J Am Heart Assoc 2017; 6(11)e007431
[37]
Coppo M, Chinenov Y, Sacta MA, Rogatsky I. The transcriptional coregulator GRIP1 controls macrophage polarization and metabolic homeostasis. Nat Commun 2016; 7: 12254.
[38]
Escate R, Padro T, Borrell-Pages M, et al. Macrophages of genetically characterized familial hypercholesterolaemia patients show up-regulation of LDL-receptor-related proteins. J Cell Mol Med 2017; 21(3): 487-99.
[39]
Mantovani A, Biswas SK, Galdiero MR, Sica A, Locati M. Macrophage plasticity and polarization in tissue repair and remodelling. J Pathol 2013; 229(2): 176-85.
[40]
Kalam H, Fontana MF, Kumar D. Alternate splicing of transcripts shape macrophage response to Mycobacterium tuberculosis infection. PLoS Pathog 2017; 13(3)e1006236
[41]
Fu Y-R, Gao K-S, Ji R, Yi Z-J. Differential transcriptional response in macrophages infected with cell wall deficient versus normal Mycobacterium tuberculosis. Int J Biol Sci 2015; 11(1): 22-30.
[42]
Gundra UM, Girgis NM, Ruckerl D, et al. Alternatively activated macrophages derived from monocytes and tissue macrophages are phenotypically and functionally distinct. Blood 2014; 123(20): e110-22.
[43]
Zhang H, Xue C, Shah R, et al. Functional analysis and transcriptomic profiling of iPSC-derived macrophages and their application in modeling Mendelian disease. Circ Res 2015; 117(1): 17-28.
[44]
Sheng K, Cao W, Niu Y, Deng Q, Zong C. Effective detection of variation in single-cell transcriptomes using MATQ-seq. Nat Methods 2017; 14(3): 267-70.
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