Combined Transcriptomic and Metabolomic Analyses Reveal the Mechanisms by Which the Interaction Between Sulfur and Nitrogen Affects Garlic Yield and Quality by Licai Ren, Xudong Pan, Yang Deng, Zhengkang Ge, Shiyuan Li, Dong Su, Guoqian Zhao, Hui Tang, Xiangfei Wang

“…However, despite the critical role of the nitrogen–sulfur interaction in garlic’s adaptability, yield, and quality, the specific mechanisms underlying these effects remain unclear. In this study, transcriptomic and metabolomic analyses were employed to investigate the effects of combined sulfur and nitrogen application on garlic bulb tissues. …”
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Integrated Metabolomic and Transcriptomic Analyses Reveal the Potential Molecular Mechanism Underlying Callus Browning in <i>Paeonia ostii</i> by Xiaohui Wen, Wenting Xu, Lili Zhang, Xiaohua Shi, Jianghua Zhou, Huichun Liu, Kaiyuan Zhu

“…In this study, we investigated the metabolites and potential regulatory genes involved in callus browning of <i>P. ostii</i> using metabolomic and transcriptomic analyses. We found a significant accumulation of phenolic compounds in the browned callus, represented by flavonoid compounds. …”
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Transcriptome analysis of nitrogen assimilation preferences in Burkholderia sp. M6-3 and Arthrobacter sp. M7-15 by Ran Liu, Ran Liu, Hongyi Qin, Qian Wang, Cheng Chu, Yunbin Jiang, Huan Deng, Cheng Han, Cheng Han, Wenhui Zhong, Wenhui Zhong, Wenhui Zhong

“…Furthermore, RNA sequencing-based transcriptome analysis was used to map the metabolic pathways of the two strains and explore their explanatory potential for N preferences.ResultsThe results showed that strain M6-3 preferred to utilize NH4+ while strain M7-15 preferred to utilize NO3−. …”
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Comparative transcriptomic analysis reveals the important role of hepatic fatty acid metabolism in the acute heat stress response in chickens by Zi Mei, Zhenquan Song, Haobo Zhou, Bin Zheng, Yiwei Xiong, Zheya Sheng, Yanzhang Gong

“…Conclusions The critical role of hepatic fatty acid metabolism in mediating the acute heat stress response in chickens was revealed by a multi-tissue comparative transcriptome, and it was determined that FASN provides actionable insights into improving heat tolerance in poultry through metabolic interventions.…”
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Comparative transcriptome analysis reveals key genes associated with meiotic stability and high seed setting rate in tetraploid rice by Pincang Lv, Man Wang, Rongjie Qiu, Chang Yao, Meng Fang, Yuandong Xing, Xianhua Zhang, Yuchi He, Detian Cai, Zhaojian Song

“…Further, comparative transcriptome analysis was performed to identify genes associated with meiotic stability and high seed setting rate in PMeS line. …”
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Transcriptome and metabolome analysis of senescent rice (Oryza sativa L.) seeds: insights into the mechanism of germination vigor and seedling morphogenesis by Jingxin Huo, Dianfeng Zheng, Naijie Feng, Rui Zhang, Yingbin Xue, Aaqil Khan, Hang Zhou, Xuefeng Shen, Liming Zhao, Yifei Li, Xiaojun Liu, Junjie Liu, Jiayi Li, Wanqi Mei, Xiaole Du, Yanan Feng

“…The current study explored the underlying mechanisms that enable rice seeds to maintain high germination rates and seedling vigor after long - term storage. We employed transcriptomic and metabolomic techniques to identify metabolic changes and key genes associated with the aging of rice seeds during long - term storage. …”
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Dexamethasone’s Clinical Efficacy in Experimental Autoimmune Pancreatitis Correlates with a Unique Transcriptomic Signature, Whilst Kinase Inhibitors Are Not Effective by Ottavia Agrifoglio, Anika Kasprick, Natalie Gross, Marc Wahlig, Emilia Kauffold, Aline Woitas, Artem Vorobyev, Luise Ehlers, Ralf J. Ludwig, Katja Bieber, Robert Jaster

“…The unique gene expression profile in dexamethasone-treated mice may provide a basis for identifying new drug targets for AIP treatment.…”
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Insights into the Metabolite Profiles of Two <i>Camellia</i> (Theaceae) Species in Yunnan Province through Metabolomic and Transcriptomic Analysis by Miao Niu, Ranyang Li, Xiongyu Li, Hongyan Yang, Jianliang Ding, Xianxiu Zhou, Yuqi He, Yawen Xu, Qian Qu, Zhiwei Liu, Jiahua Li

“…Overall, these results provide statistical support for germplasm conservation and production for both <i>C. taliensis</i> and <i>C. sinensis</i>.…”
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Integrated transcriptomic and immune profiling reveals crucial molecular pathways and hub genes associated with postoperative delirium in elderly patients by Zi-han Gou, Nan Su, Xiao-chuan Li, Da-peng Ren, Shan-shan Ren, Lin Wang, Yao Wang

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Integrated Transcriptomic and Targeted Metabolomic Analysis Reveals the Key Genes Involved in Triterpenoid Biosynthesis of <i>Ganoderma lucidum</i> by Xiaolan Xu, Chunxia Li, Fangjing Wu, Shuangshuang Zhao, Tiqiang Chen, Haihong You, Yijie Lin, Xiaoxing Zou

“…Through targeted metabolomics and transcriptome correlation analysis, six TFs and two CYP450s were significantly associated with four triterpenoid components. …”
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Transcriptome analysis of gills reveal the key metabolism-related genes and pathways response to ammonia nitrogen stress in Scylla paramamosain by Chaoyue Wang, Xiao Liu, Jie Zhou, Sixiang Wang, Xia Zheng, Zehao Li, Yuanyuan Fu, Zhongwen Jin, Lei Liu

“…Subsequently, crabs were exposed to 325.13 mg/L NH4Cl for durations of 24, 48, and 96 hours, followed by transcriptome sequencing to identify differentially expressed genes (DEGs) related to ammonia nitrogen metabolism in the anterior and posterior gills of Scylla paramamosain. …”
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Metabolome and transcriptome analysis of anthocyanin biosynthesis reveal key metabolites and candidate genes in red-stemmed alfalfa (Medicago sativa) by Yaqian Zong, Zhili Zhao, Kai Zhou, Xinhui Duan, Bo Han, Chenggang He, Heping Huang, Hua Jiang

“…Result In this study, we conducted combined transcriptome and metabolome analyses on two types of alfalfa stems: space mutation red-stemmed alfalfa and non-space mutation green-stemmed alfalfa (control). …”
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Single-cell and bulk transcriptome sequencing identifies circadian rhythm disruption and cluster-specific clinical insights in colorectal tumorigenesis by Chen Liu, Jingyang Liu, Jing Shao, Xiaoman Zhao, Lin Xie, Mengyao Shang, Ying Li, Weiming Li

“…Conclusion This study not only provide new insights into the assessment of CR status in CRC patients but also develop a prognosis model based on CR-related genes, offering a new tool for personalized risk assessment in CRC.…”
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A Comparative Transcriptomic Analysis of miRNAs and Their Target Genes During the Formation of Melanin in <i>Apis mellifera</i> by Xiangjie Zhu, Yuanmingyue Tian, Mingjie Cao, Chenyu Zhu, Jiaqi Shang, Jiaqi Sun, Yiming Liu, Bingfeng Zhou, Shujing Zhou, Xinjian Xu

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Spatial transcriptomic analysis across histological subtypes reveals molecular heterogeneity and prognostic markers in early‐stage lung adenocarcinoma by Hua Geng, Wenhao Zhou, Haitao Luo, Jiaqian Wang, Shixiong Li, Congcong Song, Yujie Zhao, Meilin Xu

“…Conclusions Our results provide new insights into the link between molecular and histologic subtypes in mixed‐type lung adenocarcinomas. …”
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Transcriptomic Profiles for Elucidating Response of Bladder Intracavitary Hyperthermic Perfusion Chemotherapy in High‐Risk Nonmuscular Invasive Bladder Cancer by Zhicheng Huang, Tianhui Zhang, Jinghua Pan, Guihao Zhang, Linjun Jiang, Huiming Jiang, Pei Wan, Ying Peng, Wenchao Zou, Qinghua Liu, Nanhui Chen

“…These findings suggest that transcriptomic profiling could provide a valuable tool for predicting treatment outcomes and identifying therapeutic targets for NMIBC.…”
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Integrated Multi-Tissue Lipidomics and Transcriptomics Reveal Differences in Lipid Composition Between Mashen and Duroc × (Landrace × Yorkshire) Pigs by Mingyue Shi, Wenxia Li, Shuai Yang, Qipin Lv, Jingxian Yang, Di Sun, Guanqing Yang, Yan Zhao, Wanfeng Zhang, Meng Li, Yang Yang, Chunbo Cai, Pengfei Gao, Xiaohong Guo, Bugao Li, Guoqing Cao

“…This comprehensive analysis provides essential information for breeding strategies and meat quality improvement.…”
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High-resolution transcriptome atlas of bladder cancer highlights the functional myeloid subsets in modulating immune microenvironmentResearch in context by Jiachen Liu, Zhen Shi, Yajian Li, Jie Ma, Jiaying Yao, Zan Yuan, Yuanhao Wang, Chunyuan Yang, Xiao Li, Nianzeng Xing, Yunping Zhu, Jianhong Zhang, Li Wu

“…Interpretation: Our findings provide a high-resolution resource for BC, elucidating the functional myeloid cell states, including TREM2+ macrophages, CMA1+ mast cells, and CD1C+ DCs. …”
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Integrated Transcriptomic and Metabolomic Analyses Reveal Changes in Aroma- and Taste-Related Substances During the Withering Process of Black Tea by Bernard Ntezimana, Wenluan Xu, Yuchuan Li, Jingtao Zhou, Sujan Pathak, Yuqiong Chen, Zhi Yu, De Zhang, Dejiang Ni

“…The weighted gene co-expression network analysis (WGCNA) of DEGs showed that one module can be associated with more components and one component can be regulated by various modules. Our findings provide new insights into the quality formation of black tea during the withering process.…”
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Transcriptome and chromatin accessibility landscape of ovarian development at different egg-laying stages in taihe black-bone silky fowls by Jingyi Zhang, Yong Cui, Jiming Ruan, Haiyan Zhu, Haiping Liang, Ji Cao, Qing Wei, Jianzhen Huang

“…This study aims to explore the ovarian development status, as well as the changes in the transcriptome and chromatin accessibility landscape at different egg-laying stages of SF, in order to reveal the epigenetic regulatory mechanisms underlying ovarian development in laying hens. …”
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