Comparative Global Metabolome Profile and Transcriptome Sequence Analysis of the Rough and Smooth Peel of the Orah Mandarin (<i>Citrus reticulata</i>) by Hongming Liu, Chunrui Long, Xiaomeng Fu, Shaohua Wang, Yuqiang Lou, Jianmei Dong, Meichao Dong, Jiamei Mao, Jiandong Yang, Hongxia Yang, Yuxia Du, Xianyan Zhou

“…Our data and discussion highlight the potential mechanisms and provide a theoretical basis for the improvement of rough peel Orah mandarins.…”
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Physiology, transcriptomics, and metabolomics reveal the regulation of calcium distribution in tomato under reduced vapor pressure deficit and increased calcium fertilizer by Xuemei Yu, Luqi Niu, Yuxin Liu, Yuhui Zhang, Jianming Li, Shuhui Zhang

“…Therefore, the carbon assimilation efficiency, water transport capacity, and differential genes and metabolites regulated Ca distribution. This work provides a theoretical basis for environmental and fertilizer management in greenhouse tomato production.…”
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Synergistic Antibacterial Mechanism of Benzyl Isothiocyanate and Resveratrol Against <i>Staphylococcus aureus</i> Revealed by Transcriptomic Analysis and Their Application in Beef by Jianan Liu, Jinle Ma, Yingrui Wang, Hongshun Hao, Jingran Bi, Hongman Hou, Gongliang Zhang

“…Finally, a synergistic antimicrobial effect of this combination was also observed in fresh lean beef at 4 °C and 25 °C. These findings provide information for future studies on the synergistic antimicrobial effects of BITC and RES on <i>S. aureus</i>.…”
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Integrated Transcriptomic Analysis of Liver and Muscle Tissues Reveals Candidate Genes and Pathways Regulating Intramuscular Fat Deposition in Beef Cattle by Siwei Wang, Tingting Liu, Peng Peng, Yurong Fu, Shaoqing Shi, Shuang Liang, Xi Chen, Kun Wang, Rongyan Zhou

“…The reliability of the transcriptomic data was verified by quantitative reverse real-time PCR (qRT-PCR). …”
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Transcriptomic analyses reveal new genes and networks response to H5N1 influenza viruses in duck (Anas platyrhynchos) by Yin-hua HUANG, Hua-peng FENG, Li-ren HUANG, Kang YI, En-guang RONG, Xiao-yun CHEN, Jian-wen LI, Zeng WANG, Peng-yang ZHU, Xiao-juan LIU, Xiao-xue WANG, Jia-xiang HU, Xin LIU, Hua-lan CHEN, Jun WANG, Ning LI

“…These analyses, in combination with our comprehensive transcriptomic data, provided global view of the molecular architecture for the interaction between host and H5N1 viruses.…”
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Identification of a prognostic signature consisting of three macrophage-related genes for glioblastoma based on bulk and single-cell transcriptomes analyses by Qiyan Wu, Chuanbiao Chen, Lina Li, Hongyu Liu, Lingling Cui, Yang Bai, Liping Zhang, Lingxiong Wang, Yaojun Peng

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A detailed transcriptome study uncovers the epigenetic characteristics associated with Aromatase inhibitor-induced masculinization in Takifugu rubripes larvae gonads by Xufang Shen, Hongwei Yan, Mingtao Hu, Huiting Zhou, Qi Zhang, Rui Gao, Qi Liu, Qunwen Sun

“…Here, to further explore the underlying regulation mechanism of AI-induced masculinization, a whole-transcriptome analysis comparing was conducted between AI-induced masculinized XX (AI-XX) gonads and control (Con) gonads in T. rubripes. …”
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Comparative enzymatic browning transcriptome analysis of three apple cultivars unravels a conserved regulatory network related to stress responses by F. J. Bielsa, J. Grimplet, P. Irisarri, C. Miranda, P. Errea, A. Pina

“…In this study, three apple cultivars with different EB phenotypes ranging from low to high browning in apple pulp were used to study transcriptomic changes over time after fresh cutting (0, 30 and 60 min). …”
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Genome Sequencing and Comparative Transcriptomic Analysis of Rice Brown Spot Pathogen <i>Bipolaris oryzae</i> Adaptation to Osmotic Stress by Chun Wang, Kexin Yang, Sauban Musa Jibril, Ruoping Wang, Chengyun Li, Yi Wang

“…This study provides a valuable foundation for understanding the pathogenic mechanisms of rice brown spot and future disease control strategies.…”
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Integrated transcriptomics and metabolomics reveal the molecular characteristics and metabolic regulatory mechanisms among different muscles in Minxian black fur sheep by Huihui Wang, Zilong Liu, Hai Yang, Yaqin Bai, Qiao Li, Xingcai Qi, Dengpan Li, Xingxu Zhao, Youji Ma

“…Results In this study, the muscle samples (Biceps femoris; longissimus dorsi; and infraspinatus) from Minxian black fur sheep were used to perform transcriptome and metabolome analyses. Then, the key genes regulating the metabolism of important flavor precursors (amino acids and lipids) were explored by integrating transcriptome and metabolome. …”
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Transcriptome-Based Analysis of the Co-Expression Network of Genes Related to Nitrogen Absorption in Rice Roots Under Nitrogen Fertilizer and Density by Runnan Wang, Qi Zhu, Haiyuan Wang, Qiangqiang Xiong

“…Based on this, we further integrated transcriptome and co-expression network analysis, revealing 40,218 expressed genes with differential expression patterns across treatments. …”
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Integrated single-cell and bulk transcriptomic analysis identifies a novel macrophage subtype associated with poor prognosis in breast cancer by Qing Wang, Yushuai Yu, Liqiong Ruan, Mingyao Huang, Wei Chen, Xiaomei Sun, Jun Liu, Zirong Jiang

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Transcriptome and Metabolome Analyses Reveal the Mechanism of Color Differences in Pomegranate (<i>Punica granatum</i> L.) Red and White Petals by Yong Zhang, Peng Han, Ruijie Zhao, Shuhan Yu, Hang Liu, Shuren Ji, Wei Chen

“…The research results provide a basis for the theory of pomegranate petal color formation.…”
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Comparative Transcriptome Profiling Reveals Differential Defense Responses of Resistant and Susceptible <i>Phalaenopsis</i> to <i>Dickeya fangzhongdai</i> by Jingjing Xin, Jiyong Tang, Ying Mao, Dongdong Ren, Ping Luo, Yongyi Cui

“…To explore the molecular mechanisms underlying disease resistance, transcriptome analysis was conducted on resistant and susceptible <i>Phalaenopsis</i> varieties. …”
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Dynamic changes and transcriptome analyses reveal the microfilament skeleton response to water stress in thalli of Neopyropia yezoensis inhabiting the intertidal zone by Jiqiang Yin, Ying Sun, Xinping Miao, Jiaxin Qu, Kunjie Zhang, Xue qing Han, Yichi Li, Jiahui Sun, Fanna Kong

“…Furthermore, this research will provide valuable insights into the species distribution of intertidal zones.…”
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Integration of graph neural networks and transcriptomics analysis identify key pathways and gene signature for immunotherapy response and prognosis of skin melanoma by Maodong Ye, Shuai Ren, Huanjuan Luo, Xiumin Wu, Hongwei Lian, Xiangna Cai, Yingchang Ji

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Identification of long noncoding RNAs (lncRNAs) and co-transcriptional analysis of mRNAs and lncRNAs in transcriptomes of Anopheles gambiae by Jiannong Xu, Kai Hu, Michelle M. Riehle, Vedbar S. Khadka

“…IntroductionAnopheles gambiae is a primary malaria vector mosquito in Africa. RNA-seq based transcriptome analysis has been widely used to study gene expression underlying mosquito life traits such as development, reproduction, immunity, metabolism, and behavior. …”
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Transcriptomic profiles of Crandell-Rees feline kidney cells infected with Varicellovirus felidalpha-1 (FHV-1) field and vaccine strains by Emily Kwan, Alistair R. Legione, Carol A. Hartley, Joanne M. Devlin

“…Conclusions This study demonstrates the host and viral gene expressions during FHV-1 infection shows the distinct host responses to field and vaccine strains using an in vitro model. These findings provide a foundation for future transcriptomic investigations in other cell types, including ex-vivo explants systems, to enhance our understanding of host and viral factors contributing to disease outcomes.…”
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Transcriptome Analysis of Effect of Cordyceps militaris Aqueous Extract in Human Gastric Cancer Cell BGC-823 on Different RCD Pathways by Mingqi CUI, Kaiwen YU, Yang SONG, Fangxu XU, Shenghou WANG, Ze WANG

“…These findings provide theoretical support for using C. militaris in functional foods.…”
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Transcriptome–Metabolome Analysis Reveals That Crossbreeding Improves Meat Quality in Hu Sheep and Their F₁-Generation Sheep by Liwa Zhang, Xuejiao An, Zhenfei Xu, Chune Niu, Zhiguang Geng, Jinxia Zhang, Haina Shi, Zhenghan Chen, Rui Zhang, Yaojing Yue

“…The results of this study offer valuable insights into the molecular mechanisms underlying the impact of crossbreeding on meat quality and provide a theoretical foundation for sheep crossbreed production.…”
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