Transcriptome analysis and genome-wide identification of WRKY gene family in Leonurus japonicus under drought stress by Tongtong Guo, Qing Wang, Yuxiao Yi, Zelin Yin, Lili Xu, Fengtang Yang, Jianing Xu, Ming Zhang

“…Results The physiological experiment results showed that drought stress significantly increased the malondialdehyde (MDA), proline, and hydrogen peroxide (H₂O₂) content of L. japonicus. Transcriptome analysis revealed significant changes in the expression levels of the WRKY gene family. …”
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Enhancing effect of 5-azacytidine on saline–alkaline resistance of Akebia trifoliata and underlying physiological and transcriptomic mechanisms by Xiao Xu Bi, Kai Wang, Xiaoqin Li, Jiao Chen, Jin Yang, Jin Yan, Guijiao Wang, Yongfu Zhang

“…Furthermore, comparative transcriptome sequencing was performed. The results demonstrated that growth and development of A. trifoliata were severely inhibited under saline–alkaline stress, suggesting that the seedlings were exposed to severe oxidative and osmotic stresses. …”
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Deciphering the regulatory programs of RNA binding proteins in rheumatoid arthritis through single-cell transcriptome analysis by Hongbin Luo, Qunya Zheng, Youzheng Zhou, Weipeng Lai, Nanwen Zhang, Peng Chen

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Combined Transcriptome Analysis Reveals the Mechanism of ‘Shine Muscat’ Pollen Abortion Induced by CPPU and TDZ Treatment by Mengfan Ren, Yixu Wang, Siyi Yi, Jingyi Chen, Wen Zhang, Haoran Li, Ke Du, Jianmin Tao, Huan Zheng

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Development and application of a whole transcriptome sequencing assay for the detection of gene fusions in clinical cancer specimens by Songchen Zhao, Xinhua Du, Yan Zhang, Jing Bai, Lu Meng, Xuefei Li, Jiaxin Ma, HeYu Sheng, Xiaorui Fu, Yanfang Guan, Yuting Yi, Ling Yang, Xuefeng Xia, Xin Yi, Xinxin Tan, Caicun Zhou

“…However, the performance characteristics of whole transcriptome sequencing (WTS) for the detection of gene fusions have not been thoroughly investigated. …”
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Single-Nucleus and Spatial Transcriptomics Revealing Host Response Differences Triggered by Mutated Virus in Severe Dengue by Qian Chen, Yizhen Yuan, Fangzhou Cai, Zhe Li, Qiang Wei, Wei Wang

“…Second, employing single-nucleus and spatial RNA sequencing, we analyzed and verified transcriptome samples in uninfected, mild (NGC group), and severe (N10 group) liver tissues from murine models. …”
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Spatial Transcriptomics Reveals Regional and Temporal Dynamics of Gene Expression in the Mouse Brain Across Development and Aging by Benjamin Conacher, Amanda Moore, Liduo Yin, Yu Lin, Xiguang Xu, Qinwen Mao, Hehuang Xie

“…Investigating transcriptomic changes during healthy development and aging provides insights into the molecular mechanisms that regulate the maturation of brain functions and drive age-related decline. …”
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Integrated transcriptomic and metabolomic analysis reveals the effects of forchlorfenuron and thidiazuron on flavonoid biosynthesis in table grape skins by Ting Zheng, Pengcheng Zhao, Jiang Xiang, Lingzhu Wei, Wanting Shen, Jiang Wu, Jianhui Cheng

“…Both CPPU and TDZ increased flavonoid content, and CPPU accelerated coloring. Combined with transcriptome analysis, cluster analysis showed that treatments T3 (two CPPU applications) and T5 had the strongest correlation. …”
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Integrating genome‐ and transcriptome‐wide association studies to uncover the host–microbiome interactions in bovine rumen methanogenesis by Wei Wang, Zhenyu Wei, Zhuohui Li, Jianrong Ren, Yanliang Song, Jingyi Xu, Anguo Liu, Xinmei Li, Manman Li, Huimei Fan, Liangliang Jin, Zhannur Niyazbekova, Wen Wang, Yuanpeng Gao, Yu Jiang, Junhu Yao, Fuyong Li, Shengru Wu, Yu Wang

“…Here, we uncover the host genetic basis of rumen microorganisms by genome‐ and transcriptome‐wide association studies with matched genome, rumen transcriptome, and microbiome data from a cohort of 574 Holstein cattle. …”
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GWAS and transcriptome analyses unravel ZmGRAS15 regulates drought tolerance and root elongation in maize by Dongmei Wang, Xuyang Liu, Guanhua He, Kailiang Wang, Yongxiang Li, Honghui Guan, Tianyu Wang, Dengfeng Zhang, Chunhui Li, Yu Li

“…Conclusion This study provides valuable information for understanding the genetic basis of drought tolerance and gene resources for maize drought tolerance breeding.…”
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Integrating network toxicology, transcriptomics, and metabolomics uncovers the hepatotoxic mechanisms of okadaic acid in LO2 cells by Zhiqiang Luo, Fulu Pan, Huixia Fan, Ruofan Guo, Jingqi Zheng, Shuo Zhang, Jiaru Shi, Wei Lin, Chen Wang, Yanli Pan, Guohua Yu

“…In summary, these findings provide valuable insights into the mechanisms underlying OKA-induced hepatotoxicity, emphasizing the integration of network toxicology, transcriptomics, and metabolomics as a novel strategy for studying the action modes of biotoxins.…”
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Combined transcriptome and metabolome analysis of stable knockdown and overexpression of the CD8A gene in chicken T lymphocytes by Yanli Du, Kun Wang, Xiannian Zi, Xiao Wang, Meiquan Li, Bo Zhang, Jinshan Ran, Wei Huang, Jing Wang, Cuilian Dong, Hanyi Xiang, Li Lei, Changrong Ge, Yong Liu

“…Thus, CD8A may be a critical regulator of “Glutathione metabolism” and may subsequently affect T-cell function in chickens. These results provide an important reference for further research on the effect of CD8A on the immune performance of chickens.…”
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Transcriptomics-based exploration of ubiquitination-related biomarkers and potential molecular mechanisms in laryngeal squamous cell carcinoma by Qiu Chen, Zhimin Wu, Yifei Ma

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A cross-tissue transcriptomic approach decodes glucocorticoid receptor-dependent links to human metabolic phenotypes by Marcin Piechota, Mateusz Zieba, Małgorzata Borczyk, Slawomir Golda, Jacek Hajto, Urszula Skupio, Michal Slezak, Jan Rodriguez Parkitna, Michal Korostynski

“…Overall effects of GR stimulation are well coordinated and closely linked to biological roles of tissues and organs. Our findings provide novel insights into complex systemic and tissue-specific actions of glucocorticoids and their potential impacts on human physiology and pathology.…”
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Mendelian randomization analysis of inflammatory biomarkers and hepatocellular carcinoma risk: genetic causality and single-cell transcriptomics by GuangXin Shao, Xiao Yun, Hongyue Xie, Beicheng Sun

“…Conclusions This study provides robust genetic evidence for causal relationships between specific inflammatory biomarkers and HCC risk through MR analysis.…”
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Revealing gene expression links between milk fat globules and mammary glands in rodents via transcriptomics by Hancai Jiang, Xiaoxian Xu, Xinhui Song, Qingyou Liu, Kuiqing Cui, Hui Li, Jieping Huang, Zhipeng Li

“…Therefore, this study aimed to utilize whole transcriptome sequencing to investigate the gene expression profiles of Golden hamsters (Gh, n = 5) and Kunming mice (Km, n = 5). …”
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A global overview of transcriptome dynamics during the late stage of flower bud development in Camellia oleifera by Huiyun Song, Zhihao Duan, Heqiang Huo, Xiaoling Wang, Yujuan Wang, Junhui Chen, Liang Jin, Mengfei Lin

“…Transcriptome analysis indicated that C.oleifera primarily regulates the late stages of flower bud development via regulating genes involved in starch and sucrose metabolism in petals, monoterpene synthesis and ABC transporters in pistils and stamens. …”
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Transcriptomic and Metabolomic Analysis Reveals Multifaceted Impact of Gcn5 Knockdown in <i>Drosophila</i> Development by Youfeng Li, Yue Xu, Ruike Li, Sirui Huang, Qiong Wu, Jing Yan, Zhigang Jiang, Xiushan Wu, Fang Li, Yuequn Wang, Yongqing Li, Xiongwei Fan, Wuzhou Yuan

“…<b>Conclusions:</b> These findings deepen our understanding of Gcn5’s roles in <i>Drosophila</i> development and provide valuable insights for developing Gcn5-targeted therapies, particularly considering its involvement in various human diseases.…”
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The molecular mechanism of ovary development in Thamnaconus septentrionalis induced by rising temperature via transcriptomics and metabolomics analysis by Yan Liu, Yan Liu, Yan Liu, Wengang Xu, Wengang Xu, Wengang Xu, Xueli Zhang, Jiulong Wang, Jiulong Wang, Jiulong Wang, Xiaoling Chen, Xiaoyan Yu, Jun Zeng, Yanqing Wu, Liming Liu, Liming Liu, Liming Liu

“…The present study for the first time elucidated the potential molecular regulatory mechanism of ovary development in T. septentrionalis induced by temperature and will provide valuable information for the artificial breeding of T. septentrionalis and conservation of T. septentrionalis fishery resources in the future.…”
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Comparative transcriptome analysis of oat varieties with different flowering performances under a short-day photoperiod by Man Zhang, Yuan Jiang, Haixiao Dong, Xiaohui Shan, Hao Chen, Xueying Li, Chunlong Wang, Sangpingcuo Ba, Junwei Li, Laichun Guo, Yaping Yuan, Changzhong Ren

“…Results In this study, we compared the developmental stages of shoot apical meristems (SAMs) and transcriptome profiles between the photoperiod-insensitive oat cultivar VAO-8 and the photoperiod-sensitive oat cultivar Baiyan 2 at four time points under a short-day photoperiod. …”
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