Regulation of neutrophil senescence by microRNAs. by Jon R Ward, Paul R Heath, James W Catto, Moira K B Whyte, Marta Milo, Stephen A Renshaw

“…Neutrophils are rapidly recruited to sites of tissue injury or infection, where they protect against invading pathogens. …”
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RETRACTED ARTICLE: Multi-stage biomedical feature selection extraction algorithm for cancer detection by Ismail Keshta, Pallavi Sagar Deshpande, Mohammad Shabaz, Mukesh Soni, Mohit kumar Bhadla, Yasser Muhammed

“…Early cancer detection is greatly aided by machine learning and artificial intelligence (AI) to gene microarray data sets (microarray data). Despite this, there is a significant discrepancy between the number of gene features in the microarray data set and the number of samples. …”
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NuMA overexpression in epithelial ovarian cancer. by Anke Brüning-Richardson, Jaqueline Bond, Rawiah Alsiary, Julie Richardson, David A Cairns, Luci McCormac, Richard Hutson, Philip A Burns, Nafisa Wilkinson, Geoff D Hall, Ewan E Morrison, Sandra M Bell

“…Aneuploidy status in primary cultures was determined by FACS analysis.Affymetrix microarray data indicated that NuMA was overexpressed in tumour tissue, primary cultures and cell lines compared to normal ovarian tissue. …”
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Spheroid Culture of Mesenchymal Stem Cells by Zoe Cesarz, Kenichi Tamama

“…Compared with traditional 2D adherent cell culture, 3D spheroidal cell aggregates, or spheroids, are regarded as more physiological, and this technique has been exploited in the field of oncology, stem cell biology, and tissue engineering. Mesenchymal stem cells (MSCs) cultured in spheroids have enhanced anti-inflammatory, angiogenic, and tissue reparative/regenerative effects with improved cell survival after transplantation. …”
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Comparison of eleven methods for genomic DNA extraction suitable for large-scale whole-genome genotyping and long-term DNA banking using blood samples. by Androniki Psifidi, Chrysostomos I Dovas, Georgios Bramis, Thomai Lazou, Claire L Russel, Georgios Arsenos, Georgios Banos

“…These four methods, comprising three modified silica based commercial kits (Modified Blood, Modified Tissue, Modified Dx kits) and an in-house developed magnetic beads based protocol, were most appropriate for extracting high quality and quantity DNA suitable for large-scale microarray genotyping and also for long-term DNA storage as demonstrated by their successful application to 600 individuals.…”
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RNA-Seq profiling reveals novel hepatic gene expression pattern in aflatoxin B1 treated rats. by B Alex Merrick, Dhiral P Phadke, Scott S Auerbach, Deepak Mav, Suzy M Stiegelmeyer, Ruchir R Shah, Raymond R Tice

“…We hypothesized RNA-Seq would reveal more differentially expressed genes (DEG) than microarray analysis, including low copy and novel transcripts related to AFB1's carcinogenic activity compared to feed controls (CTRL). …”
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The expression levels of CYP3A4 and CYP3A5 serve as potential prognostic biomarkers in lung adenocarcinoma by Mao Qixing, Xu Juqing, Wang Yajing, Dong Gaochao, Xia Wenjie, Shi Run, Wang Anpeng, Xu Lin, Jiang Feng, Wang Jun

“…Here, we explored the prognostic value of CYP3A4 and CYP3A5 in lung adenocarcinoma. The tissue microarray was made up of lung adenocarcinoma samples and corresponding normal lung tissues from Nanjing Medical University affiliated Cancer Hospital Tissue Bank. …”
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FAM111B knockdown attenuates tumorigenesis of ovarian cancer via the downregulation of MYC by Guoyu Yu, Fang Wei, Wanying Li, Qiuyun Guo, Lihong Zhang

“…Immunohistochemical analyses conducted on tissue-microarray samples obtained from patients with serous ovarian cancer indicated that elevated levels of FAM111B expression were associated with unfavorable prognostic outcomes. …”
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SMALL NONCODING RNA AS PERSPECTIVE BIOMARKERS: BIOGENESIS AND THERAPEUTIC STRATIGIES by V. V. Tiguntsev, S. A. Ivanova, V. Yu. Serebrov, M. B. Buhareva

“…The paper considers techniques to study noncoding RNA (cloning, bioinformatics analysis and hybridization methods: northern-blotting, RT-PCR, in situ hybridization, microarray analysis, reporter analysis). Possible noncoding RNA-targeted therapy can suggest delivery microRNA, anti-microRNA, antagomirs, microRNAsponges to target tissue by virus molecules, liposomes or nanoparticles.…”
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The Utilization of Formalin Fixed-Paraffin-Embedded Specimens in High Throughput Genomic Studies by Pan Zhang, Brian D. Lehmann, Yu Shyr, Yan Guo

“…Formalin fixed-paraffin-embedded (FFPE) tissue processing remains the most economical approach for longitudinal tissue specimen storage. …”
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Machine learning-based single-sample molecular classifier for cancer grading by Zoia Antysheva, Nikita Kotlov, Mariia V. Guryleva, Ivan Valiev, Viktor Svekolkin, Anna Belozerova, Sheila T. Yong, Dmitry Tabakov, Alexander Bagaev, Vladimir Kushnarev

“…While low- and high-grade tumors are predictive of patient survival for many cancers, tumors of intermediate morphological grades are considered unreliable due to interobserver variability and thus do not have clear prognostic significance. To address this issue, we devised a molecular-based classifier that uses gene expression data from RNA sequencing (RNA-seq) or microarray profiling to predict high- and low-grade risk groups for breast, lung, and renal cancers. …”
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Identification and functional analysis of light-responsive unique genes and gene family members in rice. by Ki-Hong Jung, Jinwon Lee, Chris Dardick, Young-Su Seo, Peijian Cao, Patrick Canlas, Jirapa Phetsom, Xia Xu, Shu Ouyang, Kyungsook An, Yun-Ja Cho, Geun-Cheol Lee, Yoosook Lee, Gynheung An, Pamela C Ronald

“…Using a rice NSF45K oligo-microarray to compare 2-week-old light- and dark-grown rice leaf tissue, we identified 365 genes that showed significant 8-fold or greater induction in the light relative to dark conditions. …”
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Gene Expression Profiling for In Silico Microdissection of Hodgkin's Lymphoma Microenvironment and Identification of Prognostic Features by François Bertucci, Bruno Chetaille, Luc Xerri

“…Gene expression profiling studies based on DNA microarrays have demonstrated their ability to define the interaction pathways between neoplastic and nonmalignant stromal cells in cancer tissues. …”
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Genome-wide analysis of m6A-modified circRNAs in the mouse model of myocardial injury induced by obstructive sleep apnea by Jiuhuang Lan, Yuhui Wang, Chang Liu, Hongli Chen, Qingshi Chen

“…Methods Firstly, the expression profiles of m6A-modified circRNA in left ventricular tissue of the CIH mouse model were examined using circRNA microarray analysis. …”
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Prognostic value of immune biomarkers in melanoma loco-regional metastases. by Emilia Hugdahl, Sura Aziz, Tor A Klingen, Lars A Akslen

“…In a patient series of loco-regional metastases from nodular melanomas (n = 78; n = 26 skin metastases, n = 52 lymph node metastases), expression of PD-L1 in tumour cells and the number of CD3, CD8, FOXP3 and PD-L1 positive TILs were determined by immunohistochemistry on tissue microarray (TMA) slides. Due to limited tumour tissue in the paraffin blocks, 67 of the 78 cases were included for tissue microarrays. …”
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Myofibroblast-derived extracellular vesicles facilitate cancer stemness of hepatocellular carcinoma via transferring ITGA5 to tumor cells by Yang Xiao, Ping Tao, Keke Zhang, Liuyan Chen, Jinyu Lv, Zhiwei Chen, Lu He, Hongling Jia, Jian Sun, Mingrong Cao, Jian Hong, Chen Qu

“…Methods Digital scanning and analysis of the HCC tissue microarray were performed to locate the distribution of ITGA5 and conduct the prognosis analysis. …”
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Comparative analysis of proteome and transcriptome variation in mouse. by Anatole Ghazalpour, Brian Bennett, Vladislav A Petyuk, Luz Orozco, Raffi Hagopian, Imran N Mungrue, Charles R Farber, Janet Sinsheimer, Hyun M Kang, Nicholas Furlotte, Christopher C Park, Ping-Zi Wen, Heather Brewer, Karl Weitz, David G Camp, Calvin Pan, Roumyana Yordanova, Isaac Neuhaus, Charles Tilford, Nathan Siemers, Peter Gargalovic, Eleazar Eskin, Todd Kirchgessner, Desmond J Smith, Richard D Smith, Aldons J Lusis

“…We have examined this issue using a genetic approach in which natural variations were used to perturb both transcript levels and protein levels among inbred strains of mice. …”
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Inference of cell type content from human brain transcriptomic datasets illuminates the effects of age, manner of death, dissection, and psychiatric diagnosis. by Megan Hastings Hagenauer, Anton Schulmann, Jun Z Li, Marquis P Vawter, David M Walsh, Robert C Thompson, Cortney A Turner, William E Bunney, Richard M Myers, Jack D Barchas, Alan F Schatzberg, Stanley J Watson, Huda Akil

“…Despite this, transcriptomic analyses of the human brain have typically been conducted using macro-dissected tissue due to the difficulty of performing single-cell type analyses with donated post-mortem brains. …”
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Transcriptomic analysis of laser-capture microdissected tumors reveals RAD51AP1 as a tumor-specific marker associated progression from pancreatic intraepithelial neoplasia to invas... by Fereshteh Rezagholizadeh, Adel Salimi, Ali Sharifi-Zarchi, Farid Azmoudeh-Ardalan, Kazem Mousavizadeh, Fatemeh Tajik, Mahshid Panahi, Hossein Khorramdelazad, Masoud Baghai Wadji, Atefeh Kashanizadeh, Alireza Lotfalizadeh, Seyed Javad Mowla, Mohammad Taghi Joghataei

“…Immunohistochemistry (IHC) on 353 PDAC patients, including 73 PanIN lesions and 280 tumor tissues on tissue microarray (TMA) slides, provided further confirmation. …”
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Genetic and physiological activation of osmosensitive gene expression mimics transcriptional signatures of pathogen infection in C. elegans. by Anne-Katrin Rohlfing, Yana Miteva, Sridhar Hannenhalli, Todd Lamitina

“…Here, we show that infection-activated transcriptional responses are, in large part, recapitulated by either physiological or genetic activation of the osmotic stress response. Microarray profiling of wild type worms exposed to non-lethal hypertonicity identified a suite of genes that were also regulated by infection. …”
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