Deciphering drought response mechanism in Tibetan qingke through comprehensive transcriptomic and physiological analysis by Deyuan Jiang, Deyuan Jiang, Shuaihao Chen, Shuaihao Chen, Shuaihao Chen, Zhongmengyi Qin, Zhongmengyi Qin, Zhongmengyi Qin, La Bo, La Bo, La Bo, Liping Niu, Liping Niu, Liping Niu, Hongkang Zhou, Hongkang Zhou, Jing Wang, Jing Wang, Jing Wang, Dawa Dondup, Xin Hou, Xin Hou, Xin Hou

“…These findings substantially advance our mechanistic understanding of drought adaptation in qingke while providing novel insights and valuable genetic resources for molecular breeding programs targeting abiotic stress resistance in barley and related cereal crops.…”
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Elicitor-induced stilbene production and lignin reduction in peanut hairy roots: Insights from transcriptomic and metabolomic analysis by Apinun Limmongkon, Phadtraphorn Chayjarung, Chanyanut Pankaew, Sompop Pinit, Nitra Nuengchamnong, Chonnikan Tothong

“…Phenolic, flavonoid, and stilbene levels rose, while lignin content decreased over time. Transcriptomic analysis revealed upregulation of key genes in the phenylpropanoid pathway, including PAL, C4H, and 4CL, which correlated with elevated levels of hydroxybenzoic acid and related compounds. …”
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Exploring the landscape of Parkinson’s disease transcriptomics: a quantitative review of research progress and future directions by Yiran Wang, Yiran Wang, Yiran Wang, Tong Li, Xiaoqing Zhang, Xiaoqing Zhang, Haoran Tai, Haoran Tai, Weihong Li, Weihong Li, Bingyin Su, Bingyin Su

“…IntroductionThis study leverages bibliometric analysis to uncover the research landscape and spotlight emerging trends in the field of Parkinson’s disease (PD) transcriptomics.MethodsThe relevant literature on Parkinson’s disease and transcriptomics was retrieved from the Web of Science Core Collection database. …”
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Myocardial damage post short-term self-administration cocaine usage in rat by Muhammad Zubair Saleem, Tian Liu, Ningjing Song, Jayme McReynolds, Chen Gao

“…Cocaine abuse remains a significant risk with profound adverse impact on cardiovascular health. While long-term cocaine addiction-induced cardiotoxicity is well-documented, the underlying mechanism and the molecular effects of short-term recreational usage of cocaine on the heart have not been well studied. …”
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Investigation of the Molecular Mechanism of Asthma in Meishan Pigs Using Multi-Omics Analysis by Weilong Tu, Hongyang Wang, Yingying Zhang, Ji Huang, Yuduan Diao, Jieke Zhou, Yongsong Tan, Xin Li

“…We investigated asthma pathogenesis in Meishan pigs through transcriptomic and metabolomic analyses of blood samples taken during autumn and winter. …”
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Combined metabolome and transcriptome analysis revealed that MSTN regulated the process of bovine fatty acid metabolism in gut by Li Gao, Yong Ma, Lili Wang, Hao Wu, Ruobing Kang, Guangpeng Li, Lei Yang, Tong Wen

“…Transcriptome results showed that the expression level of 1541 genes were influenced by MSTN disruption, including 536 upregulated genes and 1005 downregulated genes, which were categorized into 311 KEGG signaling pathways, primarily related to disease and metabolism. …”
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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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Predicting antimicrobial mechanism-of-action from transcriptomes: A generalizable explainable artificial intelligence approach. by Josh L Espinoza, Chris L Dupont, Aubrie O'Rourke, Sinem Beyhan, Pavel Morales, Amy Spoering, Kirsten J Meyer, Agnes P Chan, Yongwook Choi, William C Nierman, Kim Lewis, Karen E Nelson

“…We evaluated our methods using whole transcriptome responses from Escherichia coli challenged with 41 known antibiotics and 9 crude extracts while depositing 122 transcriptomes unique to this study. …”
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Combined metabolome and transcriptome to analyze the regulatory network of key enzymes in the synthesis of senkirkine in Emilia sonchifolia by Jinli Yao, Yanqing Qin, Dongping Tu, Yumei Huang, Liuguan Liang, Wenhui Cai, Mingli Huang, Xiaoqi Zhu, Xinling Lao

“…Through qRT-PCR of five key enzyme genes, researchers found that four genes (BAHD-Ats, CCoAOMT, BOMT, 3AT) peaked in roots, while CAD showed highest expression in stems—findings consistent with transcriptomic results. …”
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Physiological and Transcriptome Analyses of Gill and Hepatopancreas of <i>Potamocorbula ustulata</i> Under Ammonia Exposure by Jing He, Xinhui Wang, Mingyu Wu, Zhihua Lin, Lin He, Xiafei Zheng

“…By 96 h, DEGs in the gills were associated with nitrogen metabolism and transport, while those in the hepatopancreas were linked to oxidative phosphorylation and amino acid metabolism. …”
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Bronchoalveolar lavage single-cell transcriptomics reveals immune dysregulations driving COVID-19 severity. by Clinton Njinju Asaba, Razieh Bitazar, Patrick Labonté, Terence Ndonyi Bukong

“…Genes such as MCL1 and HIF1α supported extended viability, while MSR1 and MRC1 indicated reduced phagocytosis. …”
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Transcriptome and Metabolome Insights into Key Genes Regulating Fat Deposition and Meat Quality in Pig Breeds by Suthar Teerath Kumar, Yunlong Zheng, Jing Xu, Ziyi Zhao, Qi Zhang, Yunpeng Zhang, Min Li, Hong Zou, Riaz Muhammad Azeem, Wu-Sheng Sun, Yuan Zhao, Shu-Min Zhang

“…Transcriptome analysis identified 134 upregulated and 362 downregulated genes in the SBP. …”
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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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Transcriptomic Profile of Early Antral Follicles: Predictive Somatic Gene Markers of Oocyte Maturation Outcome by Alessia Peserico, Barbara Barboni, Chiara Camerano Spelta Rapini, Chiara Di Berardino, Giulia Capacchietti, Angelo Canciello, Fani Konstantinidou, Marisa Donato, Liborio Stuppia, Valentina Gatta

“…Meiosis resumption involved ECM remodeling, hypoxia, and relaxin signaling activation, while proliferative and metabolic pathways were downregulated. …”
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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

“…Abstract Background Salicylic acid (SA) is a key phytohormone involved in regulating plant growth, development, and immune responses. While its signaling roles have been extensively characterized in model species, the molecular mechanisms and SA-responsive genes in potato remain largely uncharacterized. …”
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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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Identifying candidate genes associated with hippocampal dysfunction in a hemiparkinsonian rat model by transcriptomic profiling by Bohye Kim, Sungmoo Hong, Jeongmin Lee, Sohi Kang, Joong-Sun Kim, Chaeyong Jung, Taekyun Shin, BuHyun Youn, Changjong Moon

“…Striatal 6-hydroxydopamine (6-OHDA) infusions were performed unilaterally in the brains of adult SD rats, while dopaminergic impairments were verified in rats with 6-OHDA-lesioned striata. …”
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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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Transcriptome-wide identification and systematic analysis of the Retrotransposon genes and their roles in ginsenoside biosynthesis in Panax ginseng by Chaofan Wang, Ruicen Liu, Dinghui Wang, Li Li, Yue Jiang, Yanfang Wang, Kangyu Wang, Mingzhu Zhao, Yi Wang, Meiping Zhang

“…However, research has primarily focused on their roles in genome structure and evolution, while their basic characteristics and impact on ginsenoside biosynthesis remain largely unexplored. …”
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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

“…Particularly, transcription factor NR4A1 showed significant upregulation in response to FLASH-IR, while chromatin stability factor ELF3 was markedly downregulated following CONV-IR. …”
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