Transcriptome and Anthocyanin Profile Analysis Reveals That Exogenous Ethylene Regulates Anthocyanin Biosynthesis in Grape Berries by Min Liu, Boyuan Fan, Le Li, Jinmei Hao, Ruteng Wei, Hua Luo, Fei Shi, Zhiyuan Ren, Jun Wang

“…However, the anthocyanin profile was not affected by exogenous ethylene. Transcriptomics analysis showed that there were a total of 825 and 1399 differentially expressed genes (DEGs) 12 h and 24 h after treatment. …”
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scVAEDer: integrating deep diffusion models and variational autoencoders for single-cell transcriptomics analysis by Mehrshad Sadria, Anita Layton

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Comparative transcriptome analysis reveals key genes and signaling pathways mediated by salicylic acid in potato by Aie Chen, Beini Zhang, Huijie Wang, Jiangqing Wang, Ji Wei, Yuxin Jia, Hongyang Wang

“…Objective This study aims to elucidate the SA-mediated transcriptional network in potato by conducting a comparative transcriptomic analysis under treatments with exogenous SA and 1-aminobenzotriazole (ABT), a pan-selective cytochrome P450 inhibitor, that impairs enzymes required for salicylic acid (SA) biosynthesis. …”
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Transcriptome Analysis of the Hippocampus in Domestic Laying Hens with Different Fear Responses to the Tonic Immobility Test by Jingyi Zhang, Min Li, Liying Pan, Ye Wang, Hui Yuan, Zhiwei Zhang, Chaochao Luo, Runxiang Zhang

“…Whole hemibrains were collected for histological and immunohistochemical analyses, while hippocampal tissues underwent transcriptome sequencing. …”
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Integrative Analysis of Transcriptomic and Metabolomic Profiles Uncovers the Mechanism of Color Variation in the Tea Plant Callus by Mengna Xiao, Yingju Tian, Ya Wang, Yunfang Guan, Ying Zhang, Yuan Zhang, Yanlan Tao, Zengquan Lan, Dexin Wang

“…Furthermore, this study investigated the molecular mechanisms underlying callus color changes using transcriptomic and metabolomic approaches. Based on transcriptome analysis, it was revealed that photosynthesis and flavonoid biosynthesis pathways were significantly enriched. …”
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Comparative Transcriptomic Analysis Unveils Divergent Effects of FLASH Versus Conventional Irradiation on Skin Cells by Mengmeng Xu, Qiliang Peng, Jun Zhang, Zhiming Xu, Xinyang Cheng, Zhifei Cao, Yongsheng Zhang

“…Our comparative analysis aimed to dissect the cellular and molecular pathways influenced by these two irradiation methods. …”
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Comprehensive transcriptome analysis of developing xylem responding to artificial bending and gravitational stimuli in Betula platyphylla. by Chao Wang, Nan Zhang, Caiqiu Gao, Zhiyuan Cui, Dan Sun, Chuanping Yang, Yucheng Wang

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Clonal phylogenies inferred from bulk, single cell, and spatial transcriptomic analysis of epithelial cancers. by Andrew Erickson, Sandy Figiel, Timothy Rajakumar, Srinivasa Rao, Wencheng Yin, Dimitrios Doultsinos, Anette Magnussen, Reema Singh, Ninu Poulose, Richard J Bryant, Olivier Cussenot, Freddie C Hamdy, Dan Woodcock, Ian G Mills, Alastair D Lamb

“…Finally, a comparison of pseudo-bulked spatial transcriptomic data to adjacent sections with WGS data also demonstrated recapitulation of ground truth (entanglement = 0.35). …”
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Transcriptome and Metabolome Analysis Reveals the Effect of Temperature on the Vegetative Mycelium of <i>Morchella sextelata</i> by Xinyu Hu, Leran Ma, Junhe Liu, Tianyuan Zhang, Zhen Wang

“…Utilizing Weighted Gene Co-expression Network Analysis (WGCNA), we constructed a co-expression network that revealed hub genes and metabolites within each module. …”
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Optimization of Protoplast Preparation Conditions in <i>Lyophyllum decastes</i> and Transcriptomic Analysis Throughout the Process by Xiaobin Li, Ying Qin, Yufei Kong, Samantha Chandranath Karunarathna, Yunjiang Liang, Jize Xu

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Comparative transcriptome analysis of low- and high-latitude populations of Charybdis japonica under temperature stress by Shaolei Sun, Zhiqi He, Feijun Zhang, Zhiqiang Han

“…These results implied that the low-latitude population was more resilient to high-temperature stress, while the high-latitude population was more resilient to low-temperature stress. …”
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Integrative transcriptomic and metabolomic analysis explores the mechanisms by which ACT001 treats MAFLD in mice by Jing Liu, Yibing Zhou, Yinglun Li, Ze Chen, Xue Jiao, Jingqin Hu, Qian Wei, Yuqiang Mi, Ping Li

“…Transcriptomic analysis was performed to identify differentially expressed genes, while metabolomic analysis was used to detect differential metabolites. …”
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Transcriptome and Metabolome Analysis of Organic and Chemical Fertilizer Effects on Highland Barley Growth and Nutrient Utilization by Jiahui Yan, Hua Weng, Lu Hou, Qiang Yao, Tao He

“…In order to elucidate the mechanisms by which organic fertilizer modulates crop growth and nutrient utilization efficiency, combined transcriptomic and metabolomic analysis revealed that as the concentration of organic fertilizer increased, the differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) shifted from secondary metabolite synthesis toward nitrogen metabolism. …”
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Transcriptomic analysis reveals shared deregulated neutrophil responses in COVID-19 and idiopathic pulmonary fibrosis by Georgios Divolis, Evgenia Synolaki, Rodoula Tringidou, Argyrios Tzouvelekis, Dimitrios T. Boumpas, Panagiotis Skendros, Ioanna-Evdokia Galani

“…Methods To investigate the molecular signatures underlying neutrophil-driven pathology, we conducted transcriptome analysis in neutrophils isolated from the peripheral blood of COVID-19 patients versus healthy individuals. …”
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Transcriptome analysis of archived tumors by Visium, GeoMx DSP, and Chromium reveals patient heterogeneity by Yixing Dong, Chiara Saglietti, Quentin Bayard, Almudena Espin Perez, Sabrina Carpentier, Daria Buszta, Stephanie Tissot, Rémy Dubois, Atanas Kamburov, Senbai Kang, Carla Haignere, Rita Sarkis, Sylvie Andre, Marina Alexandre Gaveta, Silvia Lopez Lastra, Nathalie Piazzon, Rita Santos, Katharina von Loga, Caroline Hoffmann, George Coukos, Solange Peters, Vassili Soumelis, Eric Yves Durand, Laurence de Leval, Raphael Gottardo, Krisztian Homicsko, Elo Madissoon

“…Abstract Recent advancements in probe-based, full-transcriptome technologies for FFPE tissues, such as Visium CytAssist, Chromium Flex, and GeoMx DSP, enable analysis of archival samples, facilitating the generation of data from extensive cohorts. …”
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Transcriptome sequencing and anthocyanin metabolite analysis involved in leaf red color formation of Cinnamomum camphora by Xinxin Wu, Yan Li, Tong Du, Li Kang, Baolei Pei, Weibing Zhuang, Fang Tang

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The Causal Effects Between Circulating Inflammatory Proteins and Osteoarthritis: A Mendelian Randomization and Transcriptomic Analysis by Lin S, Wu C, Pan Y

“…Furthermore, we identified six key OA-related IRGs through comprehensive transcriptomic analysis, which could serve as potential diagnostic biomarkers for OA.Conclusion: This study supports the causal relationship between OA and specific circulating inflammatory proteins and develops potential OA-related inflammatory biomarkers.Keywords: osteoarthritis, circulating inflammatory proteins, Mendelian randomization study, causal relationship, inflammation-related genes, biomarker…”
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Integrated Analysis of the Metabolome and Transcriptome During Apple Ripening to Highlight Aroma Determinants in Ningqiu Apples by Jun Ma, Guangzong Li, Yannan Chu, Haiying Yue, Zehua Xu, Jiaqi Wu, Xiaolong Li, Yonghua Jia

“…Our findings revealed substantial transcriptomic and metabolomic divergence across carotenoid, terpenoid, and fatty acid metabolic pathways. …”
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Integrated Analysis of DNA Methylome and Transcriptome Reveals Regulatory Mechanism in the Longissimus Dorsi of Duroc Pigs by Shiyin Li, Yarui Gao, Lixia Ma, Wei Chen, Zhao Ma, Zhanchi Ren, Yunzhou Wang, Yongqing Zeng

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Transcriptomics combined with physiological analysis provides insights into the mechanism of resistance to Coleosporium bletiae in Bletilla striata by Qiao Liu, Xi Lu, Qiaofen Wu, Zhibiao Lu, Renjun Qin, Kui Huang, Xun Zou, Ke Xia, Yanni Yang, Shuo Qiu

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