Integrated Transcriptome and Targeted Metabolome for Resolving Flavonoid Biosynthesis in Figs (<i>Ficus carica Linn</i>.) by Junting Sun, Hadir Yishake, Ming Wang, Hao Zhang, Jie Yan

“…This study will enrich the transcriptomic data of figs and provide some help in resolving the synthesis mechanism of fig flavonoids.…”
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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

“…Understanding these mechanisms could provide insights into veterinary medicine and human asthma research. …”
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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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Integrated analysis of the transcriptome and hormone metabolome elucidates the regulatory mechanisms governing walnut bud germination by Kai Zhao, Xiaofan Wu, Bo Liang, Shuang Gao, Jieyan Yang, Yan Bai, Yaru Wang, Xin Tian, Fang Wang, Xiuqing Yang

“…Abstract The walnut (Juglans regia) is an important oilseed tree species characterized by its extensive distribution, high oil yield, and nutrient-dense kernels, which provide substantial economic benefits. However, the rising incidence of late-spring frosts, exacerbated by global climate change, has adversely affected walnut yields. …”
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Integrated metabolomics and transcriptomics reveal differences in terpenoids and the molecular basis among the roots of three Bupleurum species by Dong Wen, Hongliang Ji, Mei Rong, Yang Liu, Jiemei Jiang, Xinwei Guo, Zhihui Gao, Yanhong Xu, Jianhe Wei

“…We combined the metabolomics and transcriptomics data to investigate the relationship between metabolites and genes. …”
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Exploring the molecular basis of efficient feed utilization in low residual feed intake slow-growing ducks based on breast muscle transcriptome by Lei Wu, Zhong Zhuang, Wenqian Jia, Yongpeng Li, Yijia Lu, Minghong Xu, Hao Bai, Zhixiu Wang, Guobin Chang, Yong Jiang

“…Thirty high RFI (HRFI) and 30 low RFI (LRFI) birds were selected to evaluate their growth performance, carcass characteristics, and muscle development. Transcriptome and weighted gene co-expression correlation network analyses of pectoral muscles were conducted on six LRFI and six HRFI ducks. …”
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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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DOLPHIN advances single-cell transcriptomics beyond gene level by leveraging exon and junction reads by Kailu Song, Yumin Zheng, Bowen Zhao, David H. Eidelman, Jian Tang, Jun Ding

“…DOLPHIN not only demonstrates superior performance in cell clustering, biomarker discovery, and alternative splicing detection but also provides a distinct capability to detect subtle transcriptomic differences at the exon level that are often masked in gene-level analyses. …”
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Prognostic Value of Centrosome Replication-Related Genes in Prostate Cancer Based on Transcriptomic and Mendelian Randomization by Qizhong Lu, Yufan Wu, Qiwei Yu, Jun Ouyang

“…In this study, we utilized PCa transcriptome data from public databases and applied bioinformatics methods to identify three prognostic genes ( CDC20 , RAD51 , and TTK ) related to centrosome duplication in PCa. …”
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De Novo transcriptome assembly and annotation of the wild service tree Sorbus torminalis (L.) Crantz by Sara Pinosio, Camilla Avanzi, Francesca Bagnoli, Ilaria Spanu, Giovanni Giuseppe Vendramin, Andrea Piotti

“…This dataset was used to produce and annotate the first transcriptome assembly for S. torminalis, paving the way for future genomic research and applications in this species. …”
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Evaluating the Anticancer Potential of Ornithogalum saundersiae Saponins on Hepatocellular Carcinoma: A Transcriptome Sequencing Method by Bo XU, Ting JIANG, Wangde JIN, Xinglin JIN

“…A total of 1381 genes showed significant differences in expression as a result of transcriptome sequencing, with a majority being involved in the TNF signaling pathway. …”
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Transcriptome and Metabolome Analysis Reveals the Effect of Temperature on the Vegetative Mycelium of <i>Morchella sextelata</i> by Xinyu Hu, Leran Ma, Junhe Liu, Tianyuan Zhang, Zhen Wang

“…In this study, we used <i>Morchella sextelata</i> as the research object and employed integrated transcriptomic and metabolomic analyses to evaluate the effects of cultivation temperatures set at 33 °C, 20 °C, and 4 °C on the vegetative mycelium of <i>Morchella</i>. …”
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Exploring the diversity of galls on Artemisia indica induced by Rhopalomyia species through morphological and transcriptome analyses by Seiji Takeda, Makiko Yoza, Sawako Ueda, Sakura Takeuchi, Akiteru Maeno, Tomoaki Sakamoto, Seisuke Kimura

“…Abstract Plant galls generated by insects have highly organized structures, providing nutrients and shelter to the insects living within them. …”
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Optimization of Fermentation and Transcriptomic Analysis: The Impact of Aspartic Acid on the Antioxidant Activity of <i>Termitomyces</i> by Jingfei Zhou, Wenhui Yi, Yunfan Yang, Jiahui Peng, Wujie Zhong, Xuefeng Xu

“…This study is the first to elucidate the molecular network by which Asp enhances the antioxidant activity of <i>Termitomyces</i>, thereby providing a foundation for its development as a natural antioxidant.…”
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Joint analysis of whole-genome methylation and transcriptome in avian pullorum disease and validation of gene function by Jiongwen Wu, Weiming Liang, Aijun Liu, Xiaomeng Wang, Zhexia Fan, Xuerong Ma, Shuya Chen, Cheng Fang, Xiquan Zhang, Qingbin Luo

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In-depth analysis of 17,115 rice transcriptomes reveals extensive viral diversity in rice plants by Yu Zhu, Ali Raza, Qing Bai, Chengwu Zou, Jiangshuai Niu, Zhongxin Guo, Qingfa Wu

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Identification and validation of differentially expressed genes in allergic asthma pathogenesis using whole-transcriptome sequencing by Fang Cui, Rui Liu, Li Wang, Jing He, Yanxia Xu

“…Differential gene expression was analyzed using DESeq2 software, providing a rigorous statistical framework for RNA-Seq data interpretation. …”
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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

“…Using single-cell transcriptomics, we conducted a secondary data analysis of bronchoalveolar lavage fluid (BALF) from COVID-19 patients of varying severities and healthy controls to comprehensively examine immune responses. …”
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Molecular mechanisms after optic nerve injury: Neurorepair strategies from a transcriptomic perspective by Xiaxue Chen, Muyang Wei, Guangyu Li

“…In summary, single-cell transcriptomic technologies provide unprecedented insights into the molecular mechanisms underlying optic nerve injury, aiding in the identification of novel therapeutic targets. …”
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The Effect of Oral Care Product Ingredients on Oral Pathogenic Bacteria Transcriptomics Through RNA-Seq by Ping Hu, Sancai Xie, Baochen Shi, Cheryl S. Tansky, Benjamin Circello, Paul A. Sagel, Eva Schneiderman, Aaron R. Biesbrock

“…This research shows that oral care product ingredients applied at biologically relevant concentrations manifest differential effects on the transcriptomics of bacterial genes in a variety of oral periodontal pathogenic bacteria. …”
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