Transcriptome analysis of CsWOX1 mutant and overexpressing lines reveals downstream genes regulating cucumber leaf morphogenesis by Anran Zhang, Xiangbao Li, Helong Zhang, Yanxin Jiang, Qingqing Li, Junjun Shen, Zheng Li

“…Specifically, CsWOX1-OE cucumber plants exhibit leaves with a distinctive 'butterfly-shaped' appearance, while mf mutants show a rapid reduction in the area of their leaf tips. …”
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Comparative Transcriptome and Metabolome Profiling Revealed Molecular Cascade Events During the Enzymatic Browning of Potato Tubers After Cutting by Li Wang, Jianwei Shan, Jitao Liu, Kang An, Kun Yang, Chengchen Li, Xiaobo Li, Xingyao Xiong

“…Up-regulated DEGs were significantly enriched in the pathways related to phenol and lipid biosynthesis, while the down-regulated DEGs were significantly enriched in the pathways related to programmed cell death. …”
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Transcriptome analysis of mammary epithelial cell between Sewa sheep and East FriEsian sheep from different localities by Rui Li, Junru Pan, Cheng Pan, Jingjing Li, Zhenzhen Zhang, Khuram Shahzad, Yu Sun, Quzhu Yixi, Wangjie Zhaxi, Haofeng Qing, Tianzeng Song, Wangsheng Zhao

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Utilizing Microbial Inoculants to Alleviate Continuous Cropping Obstacles: Insights into the Metabolites and Transcriptomic Responses of <i>Pinellia ternata</i> by Xinyu Wang, Mohammad Murtaza Alami, Shuqi Gong, Qinglin Cheng, Chaoqun Chen, Xinghui Li, Shumei Zhong, Zhigang He, Dilin Chen, Shengqiu Feng, Shenghu Chen, Shaohua Shu

“…Correspondingly, transcriptomic analysis revealed the upregulation of phenylalanine ammonia-lyase (PAL) and other stress-related genes, confirming the metabolic shifts. …”
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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

“…The content of alliin increased by 28.48%, while the levels of abscisic acid (ABA), jasmonic acid (JA), salicylic acid (SA), and gibberellin (GA) increased by 15.82%, 12.94%, 32.34%, and 48.13%, respectively. …”
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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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Phenotypic and Transcriptomic Analysis Revealed a Lack of Risk Perception by Native Tadpoles Toward Novel Non‐Native Fish by Yuanfei Wang, Yudong Zhu, Liuyang He, Haoqi Yu, Xiuqin Lin, Jianghong Ran, Feng Xie

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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 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

“…These results indicate that ammonia nitrogen stress enhances ammonia nitrogen metabolism in the anterior gill, while inhibiting this process in the posterior gill. …”
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Metabolic and Transcriptomic-Based Characterization of <i>Streptococcus salivarius</i> ssp. <i>thermophilus</i> Snew Fermentation in Milk by Ye Wang, Haijie Zhao, Huilin Zhang, Baochao Hou, Weilian Hung, Jian He, Chao Liang, Baolei Li, Chaoxin Man, Yujun Jiang, Yu Zhang, Ling Guo

“…<i>thermophilus</i> Snew-fermented milk, as well as transcriptomic and metabolomic analyses of different fermentation stages. …”
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Deciphering salt-responsive NB-ARC genes in rice transcriptomic data: A bioinformatics approach with gene expression validation by Saputro Triono Bagus, Wardhani Fila Oxi, Sholihah Nur Fadlilatus, Ermavitalini Dini, Purnama Putut Rakhmad, Nurhidayati Tutik

“…Expression analysis revealed that LOC_Os04g43440 in Inpari 35 showed increased expression at 24 h of salt stress exposure, while LOC_Os11g15700 exhibited upregulation after 48 h. …”
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Temperature-induced variation in the transcriptome of maritime pine (Pinus pinaster Ait.) embryogenic masses modulates the phenotype of the derived plants by Javier Montero-Pau, María Amparo Pérez-Oliver, Álvaro Rodríguez-Cuesta, Isabel Arrillaga, Ester Sales

“…To elucidate the mechanisms underlying these altered phenotypes, we sequenced the transcriptome of embryonal-suspensor masses (EMs) from the three epitypes, identifying 812 differentially expressed genes (DEGs). …”
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Single-cell transcriptomics reveal the prognostic roles of epithelial and T cells and DNA methylation-based prognostic models in pancreatic cancer by Jing Du, Yaqian Zhao, Jie Dong, Peng Li, Yan Hu, Hailang Fan, Feifan Zhang, Lanlan Sun, Dake Zhang, Yuhua Zhang

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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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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 content of tea leaf alcohols and aldehydes, which are the vital contributors for greenish aroma, gradually decreased as withering time increased due to the downregulation of associated genes while the compounds related to sweet and fruity characteristics increased due to the upregulated expression of related genes. …”
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Mendelian Randomization Combined with Single-Cell Transcriptome Analysis Reveals the Role of the Key Gene PCLAF in the Pathogenesis of Atopic Dermatitis by Tao R, Chen X, Wang Y, Li S, Zhou S, Aghayants S, Yan L, Zhang Q, Zhu Z

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Transcriptome profiles of blastocysts originating from oocytes matured in follicular fluid from preovulatory follicles of greater or lesser maturity by Allyson E. Stokes, Hannah M. Clark, J. Lannett Edwards, Rebecca R. Payton, Jon E. Beever, Trevor F. Freeman, Emma A. Hessock, F. Neal Schrick, Sarah E. Moorey

“…Although no pathways were significantly enriched with differentially expressed genes, transcriptome profiles suggested improved Wnt/β-catenin signaling, metabolism, and protection from oxidative stress in blastocysts derived from oocytes matured in greater maturity follicular fluid, while potential unregulated cell growth presented in blastocysts resulting from the lesser follicle maturity treatment. …”
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Metabolome and transcriptome analysis reveal the pigments biosynthesis pathways in different color fruit peels of Clausena lansium L. Skeels by Zhichang Zhao, Mark Owusu Adjei, Ruixiong Luo, Huaping Yu, Yali Pang, Jian Wang, Yu Zhang, Jun Ma, Aiping Gao

“…Jixin fruit peel is brown (BP), while the mutant cv. Zijin had purple fruit peels (PP). …”
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Correlates of clinical benefit from immunotherapy and targeted therapy in metastatic renal cell carcinoma: comprehensive genomic and transcriptomic analysis by Sumanta Pal, Paulo Gustavo Bergerot, Nazli Dizman, JoAnn Hsu, Yung Lyou, Nicholas Salgia, Daniel Enriquez, Tyler Izatt, Jeffrey M Trent, Sara Byron

“…TERT promoter mutations were associated with NCB in the IO cohort (p=0.038); transcriptomic analysis revealed multiple differentially regulated pathways downstream of TERT. …”
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Integrative single-cell and cell-free plasma RNA transcriptomics identifies biomarkers for early non-invasive AD screening by Li Wu, Li Wu, Renxin Zhang, Renxin Zhang, Yichao Wang, Yichao Wang, Shaoxing Dai, Shaoxing Dai, Naixue Yang, Naixue Yang

“…The 34-gene panel provides non-invasive molecular insights into AD pathogenesis and early screening. While cfRNA stability challenges clinical translation, our framework highlights the potential for precision diagnostics and personalized therapeutic monitoring in AD.…”
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