Integrative bioinformatics analysis and experimental validation reveals key genes and regulatory mechanisms in the development of gout by Ye Yuan, Zhiqiang Gao, Jianhong Chen, Yuejing Liu, Jingguo Zhou

“…This study aimed to identify key genes and elucidate regulatory mechanisms underlying gout development through bioinformatics analysis combined with experimental validation.MethodsTranscriptome dataset GSE160170 and single-cell dataset GSE211783 were analyzed using differential expression analysis and weighted gene co-expression network analysis (WGCNA). …”
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Exploring the Limitations of Peripheral Blood Transcriptional Biomarkers in Predicting Influenza Vaccine Responsiveness by Luca Marchetti, Emilio Siena, Mario Lauria, Denise Maffione, Nicola Pacchiani, Corrado Priami, Duccio Medini

“…Building from previous studies, we employed a recently established algorithm for signature-based clustering of expression profiles, SCUDO, to provide new insights into why blood-derived transcriptome biomarkers often fail to predict the seroresponse to the influenza virus vaccination. …”
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Description of bacterial RNA transcripts detected in Mycobacterium tuberculosis – infected cells from peripheral human granulomas by Philip J. Moos, Allison F. Carey, Jacklyn Joseph, Stephanie Kialo, Joe Norrie, Julie M. Moyareke, Anthony Amof, Hans Nogua, Albebson L. Lim, Louis R. Barrows

“…We interpret Mtb reads associated with a cell’s UMI and transcriptome to indicate infection of that individual host cell. …”
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Triptolide Causes Spermatogenic Disorders by Inducing Apoptosis in the Mitochondrial Pathway of Mouse Testicular Spermatocytes by Jiantao Zhao, Maosheng Cao, Haisheng Yi, Guitian He, Tong Chen, Lingyun Liu, Kaimin Guo, Yin Cao, Chunjin Li, Xu Zhou, Boqi Zhang, Hongliang Wang

“…Based on the transcriptome sequencing results and relevant literature reports, further experiments were performed. …”
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Protocol for high-quality RNA sequencing, cell surface protein analysis, and genotyping in single cells using TARGET-seq+ by N. Asger Jakobsen, Sven Turkalj, Paresh Vyas

“…We describe the steps for cell isolation, the preparation of single-cell RNA-seq (scRNA-seq) and genotyping libraries, and sequencing. We also provide guidance on the analysis of single-cell genotyping, transcriptome pre-processing, and data integration.For complete details on the use and execution of this protocol, please refer to Jakobsen et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.…”
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Hepatic transcript profiling in beef cattle: Effects of rumen-protected niacin supplementation. by Gastón F Alfaro, Valentino Palombo, Mariasilvia D'Andrea, Wenqi Cao, Yue Zhang, Jonathan Beever, Russell B Muntifering, Wilmer J Pacheco, Soren P Rodning, Xu Wang, Sonia J Moisá

“…The objective of our study was to assess the effect of rumen-protected niacin supplementation on the transcriptome of liver tissue in growing Angus × Simmental steers and heifers through RNA-seq analysis. …”
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RNA sequencing reveals differential expression of mitochondrial and oxidation reduction genes in the long-lived naked mole-rat when compared to mice. by Chuanfei Yu, Yang Li, Andrew Holmes, Karol Szafranski, Chris G Faulkes, Clive W Coen, Rochelle Buffenstein, Matthias Platzer, João Pedro de Magalhães, George M Church

“…Our differential gene expression analysis obviated the need for a reference naked mole-rat genome by employing a combination of Illumina/Solexa and 454 platforms for transcriptome sequencing and assembling transcriptome contigs of the non-sequenced species. …”
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GenomicScape: an easy-to-use web tool for gene expression data analysis. Application to investigate the molecular events in the differentiation of B cells into plasma cells. by Alboukadel Kassambara, Thierry Rème, Michel Jourdan, Thierry Fest, Dirk Hose, Karin Tarte, Bernard Klein

“…Genes overexpressed in each population and the pathways encoded by these genes are provided as well as how the populations cluster together. …”
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Analysis of Streptococcus dysgalactiae subspecies equisimilis gene transcripts during experimental primate necrotizing myositis by Jesus M. Eraso, Randall J. Olsen, S. Wesley Long, Ahmad Faili, Samer Kayal, James M. Musser

“…Our results provide extensive new information about the transcriptome of SDSE in vivo and reveal numerous potential targets for future therapeutic and vaccine research.…”
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Systematic evaluation of single-cell RNA-seq analyses performance based on long-read sequencing platforms by Enze Deng, Qingmei Shen, Jingna Zhang, Yaowei Fang, Lei Chang, Guanzheng Luo, Xiaoying Fan

“…Additionally, the reliability in identifying novel isoforms and allele-specific gene/isoform expression by both platforms was verified, providing a systematic evaluation to design the sequencing strategies in single-cell transcriptome studies. …”
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Prediction of pathological grade of oral squamous cell carcinoma and construction of prognostic model based on deep learning algorithm by Tingru Shao, Peirong Ni, Chun Wang, Jiahui Li, Xiaozhi Lv

“…The deep learning model can accurately predict the pathological grade of patients with OSCC, which provides certain reference value for clinical diagnosis. …”
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Single-nucleus RNA sequencing reveals cell types, genes, and regulatory factors influencing melanogenesis in the breast muscle of Xuefeng black-bone chicken by Peng Li, Xu Wei, Qiongtao Zi, Xiangyong Qu, Changqing He, Bing Xiao, Songchang Guo

“…A comprehensive analysis of the nuclear transcriptome was conducted on the breast muscle of Xuefeng black-bone chickens, encompassing 18 distinct cell types, including melanocytes. …”
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AHL26, an AT-hook gene, negatively regulates hypocotyl growth and flowering time in Arabidopsis thaliana by Shahbaz Ahmed, Anna K. Hulbert, Xin Xin, Michael M. Neff

“…Furthermore, transcriptome analysis provides insight into the biological processes and pathways through which AHL26 influences the control of flowering time.…”
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Identification and Quantification of Carotenoids in White and Yellow-Fleshed Peaches (<i>Prunus persica</i> (L.) Batsch) by QTRAP+ LC-MS/MS by Yanfei Guo, Yonglin Jing, Qinghao Wang, Wangshu Zhang

“…Integrative metabolome-transcriptome analysis identified core regulatory networks associated with metabolic shifts, including transcription factors (<i>MYB</i> and <i>WRKY</i>). …”
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Identification of the "Collagen-Macrophage" sub-category of patients with colorectal cancer as an extension of the CMS4 subtype with THBS2 as a therapeutic target by Shuwen Chen, Zhaoyan Jiang, Wanxuan Song, Chuqiao Lu, Yanbing Lin, Shiyao Xu, Kunxin Xie, Li Wan, Xiaoqin Yuan

“…Abstract We identified a subset of patients with colorectal cancer (CRC) enriched with “collagen-TAMs,” designated the CM class, using large integrated colon cancer transcriptome and single-cell transcriptome datasets. …”
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Single-cell RNA sequencing in tuberculosis: Application and future perspectives by Yuejuan Zhan, Qiran Zhang, Wenyang Wang, Wenyi Liang, Chengdi Wang, Peifang Wei

“…Single-cell RNA sequencing (scRNA-seq) provides unbiased transcriptome sequencing of large quantities of individual cells, thereby defining biological comprehension of cellular heterogeneity and dynamic transcriptome state of cell populations in the field of immunology and is therefore increasingly applied to lung disease research. …”
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HOXD1 regulates neural crest cells differentiation and polycerate development in sheep by Cheng Zhang, Shuhong Zhang, Huifeng Xu, Guan Wang, Huan Zhang, Tenggang Di, Liming Tian, Menghan Chang, Fengyi Gao, Ming Li, Guangli Yang

“…These findings provide a theoretical basis for further investigation into the regulation of multi-horned traits growth and development in sheep.…”
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Development of Microsatellite Markers for the Nipa Palm Hispid Beetle, Octodonta nipae (Maulik) by Zhiming Chen, Jun Chen, Xiang Zhang, Youming Hou, Guihua Wang

“…The population of Zhangzhou and Fuzhou was analyzed by the 9 loci (On1–On9). These SSR transcriptome data can provide invaluable resource for SSR development, population genetics research, invasion and expansion mechanism, paternity testing, and other research on O. nipae and its related species.…”
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Adaptations of lipid metabolism in low-grade clear cell renal cell carcinoma are linked to cholesteryl ester accumulation by Olatz Fresnedo, Jose Antonio Lopez-Gomez, Carlos Ceniceros, Gorka Larrinaga, Alberto Saiz, Lorena Mosteiro, Hiart Navarro-Imaz, Yuri Rueda

“…Based on correlations between lipidome and lipometabolic transcriptome, this study provides new perspectives for evaluating pharmacological lipid management as a future therapeutic approach for low-grade ccRCC treatment.…”
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Cited1 deficiency suppresses intestinal tumorigenesis. by Valérie Méniel, Fei Song, Toby Phesse, Madeleine Young, Oliver Poetz, Lee Parry, John R Jenkins, Geraint T Williams, Sally L Dunwoodie, Alastair Watson, Alan R Clarke

“…This restraint imposed by Cited1 is consistent with a requirement for Cited1 to constrain Wnt activity to a level commensurate with optimal adenoma formation and maintenance, and provides one mechanism for tumour repression in the absence of Cited1.…”
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