Transcriptomic and biochemical insights into key gene networks driving bulbil development of Pinellia ternata (Thunb.) Breit. by Xiwei Jia, Xijia Jiu, Yuan Liu, Chao Guo, Dong Liu, Xin Zhao, Honggang Chen, Tao Du

“…Based on physiological and biochemical reactions as well as transcriptome technology, this study determined the content of endogenous metabolites and related enzyme activities during the five growth stages of the bulbils, obtained the transcriptome information of all samples. …”
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Transcriptome profiling of two rice varieties reveals their molecular responses under high night-time temperature. by Wardah K Mustahsan, Yuya Liang, Abdul R Mohammed, Charles D Johnson, Endang M Septiningsih, Lee Tarpley, Michael J Thomson

“…In this study, we employed a transcriptome approach to investigate the effects of HNT, 1-MCP, and their interaction on two Texas rice varieties, Antonio and Colorado. …”
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Identification and validation of five ferroptosis-related molecular signatures in keloids based on multiple transcriptome data analysis by Zhen Sun, Yonghong Qin, Xuanfen Zhang

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Transcriptomic and network toxicology approaches reveal potential mechanisms of DEHP induced intrahepatic cholestasis during pregnancy by Lun Zhang, Qianqian Huang, Yun Yu, Yue Jiang, Mengzhen Hou, Wenkang Tao, Cheng Zhang, Jianqing Wang

“…In conclusion, this study offers novel insights into the molecular mechanisms of DEHP-induced hepatotoxicity during pregnancy while providing a systematic framework for assessing risks associated with DEHP exposure; thus contributing to the prevention and treatment of ICP.…”
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Spatial transcriptomics and scRNA-seq: decoding tumor complexity and constructing prognostic models in colorectal cancer by Wei Song, Yatao Wang, Min Zhou, Fengqin Guo, Yanliang Liu

“…Abstract Introduction Recent advancements in transcriptomic analysis, combined with single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics, have deepened our understanding of the tumor microenvironment and cellular heterogeneity, laying the groundwork for personalized therapies. …”
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Winnow-KAN: single-cell RNA-seq location recovery with small-gene-set spatial transcriptomics by Yuyang Zhang, Qihuang Zhang

“…While these state-of-the-art methods demonstrate excellent performance in cell location recovery, their effectiveness is often specific to the particular pair of scRNA-seq and spatial transcriptomics datasets used, limiting their scalability to larger datasets and generalizability to external query scRNA-seq data. …”
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Orthologous marker groups reveal broad cell identity conservation across plant single-cell transcriptomes by Tran N. Chau, Prakash Raj Timilsena, Sai Pavan Bathala, Sanchari Kundu, Bastiaan O. R. Bargmann, Song Li

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Differential Gene Expression Analysis of Whole Blood Transcriptome Between Young and Old Border Collie Dogs by Dávid Jónás, Kitti Tátrai, Zsófia Rékasi, Balázs Egyed, Eniko Kubinyi

“…However, studies on other species, such as wolves, have identified more significant age-related genes. In conclusion, while some of our findings are promising, further research is needed to standardize environmental factors affecting blood gene expression levels in dogs. …”
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Spatial transcriptomics reveals tumor microenvironment heterogeneity in EBV positive diffuse large B cell lymphoma by Mei-yao He, Meng Liu, Jiayin Yuan, Jin Lv, Wei Li, Qianwen Yan, Yujiao Tang, Luyi Wang, Li Guo, Fang Liu

“…Here, we integrated 10X Visium spatial transcriptomics (ST) with single-cell RNA sequencing (scRNA-seq) to map TME heterogeneity in EBV+DLBCL. …”
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De Novo Assembly, Characterization and Comparative Transcriptome Analysis of the Mature Gonads in <i>Megalobrama terminalis</i> by Yicheng Zhou, Weiqian Liang, Kaifeng Wang, Peng Zheng, Shengyue Lin, Haiying Yang, Guojun Cai, Ziyan Deng, Chong Han, Qiang Li

“…This paper presents the first comparative transcriptome analysis of the gonads of female and male <i>M. terminalis</i>. …”
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Transcriptome Analysis of Resistant and Susceptible Sorghum Lines to the Sorghum Aphid (<i>Melanaphis sacchari</i> (Zehntner)) by Minghui Guan, Junli Du, Jieqin Li, Tonghan Wang, Lu Sun, Yongfei Wang, Degong Wu

“…Moench) cultivars, revealing that HX133 significantly suppressed aphid proliferation through repellent and antibiotic effects, while aphid populations increased continuously in HX37. …”
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Deciphering the dose-dependent effects of thymoquinone on cellular proliferation and transcriptomic changes in A172 glioblastoma cells. by Rachana Pandey, Purushothaman Natarajan, Umesh K Reddy, Wei Du, Cristian Sirbu, Moussa Sissoko, Gerald R Hankins

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DLX4 regulates rheumatoid arthritis fibroblast-like synoviocytes invasiveness and a cancer transcriptomic signature by Teresina Laragione, Carolyn Harris, Percio S. Gulko

“…HMOX1 and SOD2 were among the genes with the most significantly increased expression, while CPNE3 and HADHA were among those with the most significantly decreased expression in FLS knocked down for DLX4 compared with controls. …”
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Lymph node transcriptomic profiles suggest susceptibility to bleomycin-induced pulmonary toxicity in classic hodgkin lymphoma by Maja Dam Andersen, Marie Hairing Enemark, Kristina Lystlund Lauridsen, Stephen Jacques Hamilton-Dutoit, Jørn Starklint, Francesco d’Amore, Maja Ludvigsen, Peter Kamper

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XModNN: Explainable Modular Neural Network to Identify Clinical Parameters and Disease Biomarkers in Transcriptomic Datasets by Jan Oldenburg, Jonas Wagner, Sascha Troschke-Meurer, Jessica Plietz, Lars Kaderali, Henry Völzke, Matthias Nauck, Georg Homuth, Uwe Völker, Stefan Simm

“…Two crucial genes and three pathways were identified for sex classification, while 26 genes and six pathways are highly important to discriminate adrenergic–mesenchymal cell states in neuroblastoma cancer.…”
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Transcriptomic Changes of Telencephalon and Hypothalamus in Largemouth Bass (<i>Micropterus salmoides</i>) Under Crowding Stress by Meijia Li, Leshan Yang, Ying Liu

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Integration of transcriptome and Mendelian randomization analyses in exploring the extracellular vesicle-related biomarkers of diabetic kidney disease by Xu Yang, Rensong Yue, Liangbin Zhao, Qiyue Wang

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Transcriptome analysis of Bombyx mori larval midgut during persistent and pathogenic cytoplasmic polyhedrosis virus infection. by Anna Kolliopoulou, Filip Van Nieuwerburgh, Dimitrios J Stravopodis, Dieter Deforce, Luc Swevers, Guy Smagghe

“…Collectively, our data provide an initial assessment of the relative significance of persistent infection of silkworm larvae on the host response following pathogenic infection with CPV, while they also highlight the relative importance of RNAi as an antiviral mechanism.…”
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A Review of Genomic, Transcriptomic, and Proteomic Applications in Edible Fungi Biology: Current Status and Future Directions by Muyun Xie, Jing Wang, Feixiang Wang, Jinfeng Wang, Yunjin Yan, Kun Feng, Baixiong Chen

“…It discusses how these technologies, independently and in preliminary integration, uncover critical steps and regulatory mechanisms within endogenous metabolic pathways. While acknowledging the importance of metabolomics and epigenomics as cutting-edge areas, this review focuses on the “classical triad” of genomics, transcriptomics, and proteomics due to their technological maturity, data accessibility, and established application base in elucidating core metabolic mechanisms in edible fungi. …”
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In-Depth Exploration of the Coloration Mechanism of <i>Iris dichotoma</i> Pall. via Transcriptomic and Metabolomic Analyses by Yalin Yu, Xiaojing Qiang, Fan Huang, Xiuzheng Huang, Lei Liu

“…A comprehensive integrative analysis of the transcriptome and metabolome of the two petal types was carried out. …”
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