Unique Gene Expression Signatures in the Intestinal Mucosa and Organoids Derived from Germ-Free and Monoassociated Mice by Lucie Janeckova, Klara Kostovcikova, Jiri Svec, Monika Stastna, Hynek Strnad, Michal Kolar, Tomas Hudcovic, Jitka Stancikova, Jolana Tureckova, Nikol Baloghova, Eva Sloncova, Katerina Galuskova, Helena Tlaskalova-Hogenova, Vladimir Korinek

“…Analysis of the impact of various microbiota on intestinal tissue provides an important insight into the function of this organ. We used cDNA microarrays to determine the gene expression signature of mucosa isolated from the small intestine and colon of germ-free (GF) mice and animals monoassociated with two <i>E. coli</i> strains. …”
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Heat shock drives genomic instability and phenotypic variations in yeast by Li Shen, Yu-Ting Wang, Xing-Xing Tang, Ke Zhang, Pin-Mei Wang, Yang Sui, Dao-Qiong Zheng

“…Using genetic screening systems and customized single nucleotide polymorphism (SNP) microarrays, we found that heat shock (52 °C) for several minutes could heighten mitotic recombination by at least one order of magnitude. …”
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Proteomics-derived basal biomarker DNA-PKcs is associated with intrinsic subtype and long-term clinical outcomes in breast cancer by Karama Asleh, Nazia Riaz, Angela S. Cheng, Dongxia Gao, Samuel C. Y. Leung, Meenakshi Anurag, Torsten O. Nielsen

“…We evaluated DNA-PKcs expression in clinically-annotated breast cancer tissue microarrays and correlated results with immune biomarkers (training set: n = 300; validation set: n = 2401). …”
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The antibody landscapes following AS03 and MF59 adjuvanted H5N1 vaccination by Johannes B. Goll, Aarti Jain, Travis L. Jensen, Rafael Assis, Rie Nakajima, Algis Jasinskas, Lynda Coughlan, Sami R. Cherikh, Casey E. Gelber, S. Khan, D. Huw Davies, Philip Meade, Daniel Stadlbauer, Shirin Strohmeier, Florian Krammer, Wilbur H. Chen, Philip L. Felgner

“…To better understand how vaccine adjuvants AS03 and MF59 may provide improved antibody responses to vaccination, we interrogated serum from subjects who received 2 doses of inactivated monovalent influenza A/Indonesia/05/2005 vaccine with or without AS03 or MF59 using hemagglutinin (HA) microarrays (NCT01317758 and NCT01317745). The arrays were designed to reflect both full-length and globular head HA derived from 17 influenza A subtypes (H1 to H16 and H18) and influenza B strains. …”
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Global lysine methylome profiling using systematically characterized affinity reagents by Christine A. Berryhill, Jocelyne N. Hanquier, Emma H. Doud, Eric Cordeiro-Spinetti, Bradley M. Dickson, Scott B. Rothbart, Amber L. Mosley, Evan M. Cornett

“…In this study, we use peptide microarrays to show that pan-methyllysine antibodies have sequence bias, and we evaluate how the differential selectivity of these reagents impacts the detection of methylated peptides in MS-based workflows. …”
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Construction of human activity‐based phosphorylation networks by Robert H Newman, Jianfei Hu, Hee‐Sool Rho, Zhi Xie, Crystal Woodard, John Neiswinger, Christopher Cooper, Matthew Shirley, Hillary M Clark, Shaohui Hu, Woochang Hwang, Jun Seop Jeong, George Wu, Jimmy Lin, Xinxin Gao, Qiang Ni, Renu Goel, Shuli Xia, Hongkai Ji, Kevin N Dalby, Morris J Birnbaum, Philip A Cole, Stefan Knapp, Alexey G Ryazanov, Donald J Zack, Seth Blackshaw, Tony Pawson, Anne‐Claude Gingras, Stephen Desiderio, Akhilesh Pandey, Benjamin E Turk, Jin Zhang, Heng Zhu, Jiang Qian

“…Here, we developed a new strategy, called CEASAR, based on functional protein microarrays and bioinformatics to experimentally identify substrates for 289 unique kinases, resulting in 3656 high‐quality KSRs. …”
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Construction and Analysis of Gene Co-Expression Networks in Escherichia coli by Wei Liu, Li Li, Xuhe Long, Weixin You, Yuexian Zhong, Menglin Wang, Huan Tao, Shoukai Lin, Huaqin He

“…Thirty-one gene co-expression modules were detected from 1391 microarrays of E. coli data. Further characterization of these modules with the database for annotation, visualization, and integrated discovery (DAVID) tool showed that these modules are associated with several kinds of biological processes, such as carbohydrate catabolism, fatty acid metabolism, amino acid metabolism, transportation, translation, and ncRNA metabolism. …”
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Versatile and Easily Designable Polyester-Laser Toner Interfaces for Site-Oriented Adsorption of Antibodies by Marcin Drozd, Polina Ivanova, Katarzyna Tokarska, Kamil Żukowski, Aleksandra Kramarska, Adam Nowiński, Ewa Kobylska, Mariusz Pietrzak, Zbigniew Brzózka, Elżbieta Malinowska

“…This work shows for the first time a comprehensive study on the adsorption of antibodies on toner-covered poly(ethylene terephthalate) (PET@toner) substrates, together with assessment of such platforms in rapid prototyping of disposable microdevices and microarrays for immunodiagnostics. In the framework of presented research, the surface properties and antibody binding capacity of PET substrates with varying levels of toner coverage (0–100%) were characterized in detail. …”
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A novel circRNA, hsa_circ_0069382, regulates gastric cancer progression by Haoying Wang, Hao Yuan, Qinghong Guo, Xi Zeng, Mengxiao Liu, Rui Ji, Zhaofeng Chen, Quanlin Guan, Ya Zheng, Yuping Wang, Yongning Zhou

“…Therefore, we analyzed miRNA and circRNA microarrays of paired early-stage gastric cancer samples. …”
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Characterization of the Tumor Microenvironment in Jaw Osteosarcomas, towards Prognostic Markers and New Therapeutic Targets by Hélios Bertin, Sophie Peries, Jérôme Amiaud, Nathalie Van Acker, Bastien Perrot, Corinne Bouvier, Sébastien Aubert, Béatrice Marie, Frédérique Larousserie, Gonzague De Pinieux, Vincent Crenn, Françoise Rédini, Anne Gomez-Brouchet

“…Methods—We studied 50 JO biopsy samples by immunohistochemical analysis of tissue microarrays (TMAs). We investigated the bone remodeling markers RANK/RANKL/OPG, the endothelial glycoprotein CD146, and biomarkers of the immune environment (CD163 and CD68 of macrophages, CD4+ and CD8+ of tumor-infiltrating lymphocytes (TILs), and an immune checkpoint PD-1/PD-L1). …”
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A Novel Molecular Signature of Cancer-Associated Fibroblasts Predicts Prognosis and Immunotherapy Response in Pancreatic Cancer by Weiyu Ge, Ming Yue, Yanling Wang, Yongchao Wang, Shengbai Xue, Daiyuan Shentu, Tiebo Mao, Xiaofei Zhang, Haiyan Xu, Shumin Li, Jingyu Ma, Liwei Wang, Jiujie Cui

“…Firstly, we demonstrated that α-SMA⁺ CAFs were the most prominent stromal components and correlated with the poor survival rates of PC patients in our tissue microarrays. Then, we discriminated two diverse molecular subtypes (CAF clusters A and B) and revealed the significant differences in the tumor immune microenvironment (TME), four reported CAF subpopulations, clinical characteristics, and prognosis in PC samples. …”
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Patterned immobilization of polyoxometalate-loaded mesoporous silica particles via amine-ene Michael additions on alkene functionalized surfaces by Bingquan Yang, Pierre Picchetti, Yangxin Wang, Wenjing Wang, Christoph Seeger, Kliment Bozov, Sharali Malik, Dennis Mallach, Andreas H. Schäfer, Masooma Ibrahim, Michael Hirtz, Annie K. Powell

“…Specifically, we have developed a strategy that leads to water-stable, POM-loaded mesoporous silica that can be covalently linked to alkene-bearing surfaces by amine-Michael addition and patterned into microarrays by scanning probe lithography (SPL). The immobilization strategy presented facilitates the printing of hybrid POM-loaded nanomaterials onto different surfaces and provides a versatile method for the fabrication of POM-based composites. …”
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Biobanking in dentistry: A review by Stefano Sivolella, Anna Scanu, Zijing Xie, Sara Vianello, Edoardo Stellini

“…To give some examples: gene expression microarrays obtained on biobanked specimens were used in the identification of genetic alterations in oral cancer; efforts to identify genetic mechanisms behind dental caries have been based on an integrative analysis of transcriptome-wide associations and messenger RNA expression. …”
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Association Study among Comethylation Modules, Genetic Polymorphisms and Clinical Features in Mexican Teenagers with Eating Disorders: Preliminary Results by Germán Alberto Nolasco-Rosales, José Jaime Martínez-Magaña, Isela Esther Juárez-Rojop, Thelma Beatriz González-Castro, Carlos Alfonso Tovilla-Zarate, Ana Rosa García, Emmanuel Sarmiento, David Ruiz-Ramos, Alma Delia Genis-Mendoza, Humberto Nicolini

“…We used MethylationEPIC and Psycharray microarrays to determine DNA methylation levels and genotype from 63 teenagers with eating disorders. …”
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Polypyrimidine tract-binding protein 3/insulin-like growth factor 2 mRNA-binding proteins 3/high-mobility group A1 axis promotes renal cancer growth and metastasis by Qianqing Wang, Fang Chen, Yu He, Yue Gao, Jiawen Wang, Sufang Chu, Pei Xie, Jiateng Zhong, Haixia Shan, Jin Bai, Pingfu Hou

“…However, the molecular mechanisms of PTBP3 in renal cell carcinoma (RCC) remain unknown. Here, tissue microarrays (TMAs) suggested that PTBP3 expression was increased in human RCC and that high PTBP3 expression was correlated with poor five-year overall survival and disease-free survival. …”
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Spatial Manipulation of Particles and Cells at Micro- and Nanoscale via Magnetic Forces by Larissa V. Panina, Anastasiya Gurevich, Anna Beklemisheva, Alexander Omelyanchik, Kateryna Levada, Valeria Rodionova

“…Starting from simple systems of individual magnets and methods of field computation, more advanced magnetic microarrays obtained by lithography patterning of permanent magnets are introduced. …”
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Transgelin promotes lung cancer progression via activation of cancer-associated fibroblasts with enhanced IL-6 release by Chanjun Sun, Kaishang Zhang, Chen Ni, Jiajia Wan, Xixi Duan, Xiaohan Lou, Xiaohan Yao, Xiangnan Li, Ming Wang, Zhuoyu Gu, Pengyuan Yang, Zhenzhen Li, Zhihai Qin

“…Here, we find that transgelin (TAGLN) protein levels increased in primary CAFs isolated from human lung cancer, compared with those in paired normal fibroblasts. Tumor microarrays (TMAs) revealed that increased stromal TAGLN levels correlates with more lymphatic metastasis of tumor cells. …”
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microRNA Detection via Nanostructured Biochips for Early Cancer Diagnostics by Sara Martino, Chiara Tammaro, Gabriella Misso, Michela Falco, Marianna Scrima, Marco Bocchetti, Ilaria Rea, Luca De Stefano, Michele Caraglia

“…Real time-quantitative polymerase chain reaction (RT-qPCR), microarrays, and small RNA sequencing represent the gold standard techniques used in the last 30 years as detection methods. …”
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Immunohistochemical Analysis of Nicotinamide Phosphoribosyltransferase Expression in Gastric and Esophageal Adenocarcinoma (AEG) by Alexander Arnold, Moritz von Winterfeld, Erika Berg, Michael Hummel, Beate Rau, Felix Krenzien, Ulrike Stein, Christoph Treese

“…In order to study the expression levels of NAMPT in adenocarcinoma of the esophagogastric junction and stomach (AEG/S) we performed immunohistochemical analysis in a cohort of 296 tumor samples using tissue-microarrays (TMAs). In the present investigation, we saw a high expression of NAMPT in only a minority of our large AEG/S cohort. …”
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MicrobesOnline: an integrated portal for comparative and functional genomics by Dehal, Paramvir S., Joachimiak, Marcin P., Price, Morgan N., Bates, John T., Baumohl, Jason K., Chivian, Dylan, Friedland, Greg D., Huang, Katherine H., Keller, Keith, Novichkov, Pavel S., Dubchak, Inna L., Alm, Eric J., Arkin, Adam P.

“…The portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms ranging from model organisms such as Escherichia coli and Saccharomyces cerevisiae to environmental microbes such as Desulfovibrio vulgaris and Shewanella oneidensis. …”
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