Unveiling migraine subtype heterogeneity and risk loci: integrated genome-wide association study and single-cell transcriptomics discovery by Shuxu Wei, Yan Quan, Xinyi Li, Suiqin Zhong, Ling Xiao, Chao Yang, Ronghuai Shen, Xiaojia Lu, Lingbin He, Youti Zhang, Xianxi Huang

“…Methods We integrated genome-wide association study (GWAS) data from FinnGen R11 and international cohorts with transcriptomic, epigenomic, and spatially resolved single-cell spatial transcriptomics (sc-ST) profiles. …”
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Integrated single-cell and transcriptome sequencing data reveal the value of IL1RAP in gastric cancer microenvironment and prognosis by Weifeng Yang, Xiaohua Wu, Jian Wang, Wenquan Ou, Xing Huang

“…The CIBERSORT and ssGSEA algorithms elucidated immune infiltration patterns, while TIDE and TCGA predicted immune-related outcomes. …”
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Differential responses of the intestine and liver transcriptome to high levels of plant proteins in diets for large yellow croaker (Larimichthys crocea) by Qiaozhen Ke, Qiaozhen Ke, Yin Li, Huasong Weng, Baohua Chen, Jiaying Wang, Ji Zhao, Ji Zhao, Pengxin Jiang, Peng Xu, Tao Zhou

“…Results showed no significant growth performance differences between the two groups. Transcriptome analysis identified 557 and 308 differentially expressed genes in the liver and intestine respectively. …”
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Transcriptome approach to understand the potential mechanisms of resistant and susceptible alfalfa (Medicago sativa L.) cultivars in response to aphid feeding by Xiong-bing TU, Hai-long ZHAO, Ze-hua ZHANG

“…In this pilot study, we conducted a transcriptomic analysis of a resistant (R) and susceptible (S) variety of alfalfa, with (+A) or without (–A) aphids (totally four treatments). …”
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Decoding the Tissue-Specific Profiles of Bioactive Compounds in <i>Helvella leucopus</i> Using Combined Transcriptomic and Metabolomic Approaches by Qian Zhou, Xusheng Gao, Junxia Ma, Haoran Zhao, Dan Gao, Huixin Zhao

“…Transcriptomic analysis revealed a higher expression of genes involved in sterol biosynthesis (<i>ERG1</i>, <i>ERG3</i>, <i>ERG6</i>) and energy metabolism (<i>PGK1</i>, <i>ENO1</i>, <i>PYK1</i>) in the cap, suggesting a more active metabolic profile in this tissue. …”
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Transcriptomic Differences Between Human Trabecular Meshwork Stem Cells and Trabecular Meshwork Cells Reveal Specific Biomarker Profiles by Rong Du, Ajay Kumar, Enzhi Yang, Jingxue Zhang, Ningli Wang, Yiqin Du

“…A functional enrichment analysis revealed that TMSCs are associated with development, immune signaling, and extracellular matrix remodeling pathways, while TMCs are enriched in structural, contractile, and adhesion-related functions. …”
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Combined Physiological and Transcriptomic Analyses of the Effects of Exogenous Trehalose on Salt Tolerance in Maize (<i>Zea mays</i> L.) by Jingyi He, Hongliang Tang

“…This study aims to investigate the pathways and mechanisms by which trehalose mediates the improvement of salt tolerance in maize through a combined analysis of physiology and transcriptomics. The results indicate that foliar application of trehalose treatment significantly increased maize biomass and antioxidant enzyme activity while reducing the H₂O₂ and Na⁺/K⁺ ratios in both the aerial and underground parts of the plant. …”
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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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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

“…Moreover, the application of sulfur and nitrogen significantly reduced the malondialdehyde (MDA) content and peroxidase (POD) activity in garlic bulbs by 29.66% and 9.42%, respectively, thereby improving garlic’s adaptability and growth potential. Transcriptomic analysis revealed differentially expressed genes in several key pathways, including plant hormone signal transduction, RNA degradation, glutathione metabolism, amino acid biosynthesis, and glycerophospholipid metabolism. …”
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The effects of dietary curcumin on growth, antioxidant, transcriptome, and metabolomics in Macrobrachium rosenbergii fed a high plant-protein diet by Li Wang, Qincheng Huang, Zhimin Gu, Cui Liu, Xing Ren, Yangxin Dai, Tiantian Ye, Junjun Yan, Jilun Meng, Yutong Zheng, Bo Liu

“…In summary, a 10 g/kg CU supplementation in a high plant-protein diet notably augmented growth characteristics, enhanced antioxidant capacity, and improved hepatopancreas and intestinal health, while also refining transcriptome and metabolomics profiles.…”
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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

“…The differentially expressed genes and differential metabolites screened from several categories, such as carbohydrates, proteins, amino acids, fats, and fatty acids, varied at different fermentation stages, while differentially expressed genes and differential metabolites were also threaded together for joint analysis in this study. …”
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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

“…We conducted an in silico analysis of the NB-ARC gene family across three transcriptomic datasets of rice under salt stress. …”
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The hematopoietic function, histological characteristics, and transcriptome profiling of Wanxi white geese ovary during nesting and late-laying stages by Chunfang Zhao, Tao Jin, Kefeng Yang, Xinyu Liu, Man Ren, Deyong She, Qianqian Hu, Shenghe Li

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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 weighted gene co-expression network analysis (WGCNA) of DEGs showed that one module can be associated with more components and one component can be regulated by various modules. …”
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Transcriptome combined single-cell sequencing explores molecular mechanisms of ANGPTL4 in sepsis-induced acute lung injury. by Ying Qi, Changqi Zhou, Bing Chen

“…GSEA examined gene-immune cell relationships, while gene enrichment analysis explored key gene mechanisms. miRNA networks identified target miRNAs for these key genes. …”
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Transcriptomic and metabolomic analyses for the mechanism underlying anthocyanin synthesis during the growth and development of purple eggplant (Solanum melongena L) by Ting Yang, Wanping Lv, Runjie Zhuang, Shiyu Wang, Shuqi Fan, Yongxian Wen, Yongxian Wen

“…Metabolomic profiling identified anthocyanin types, while transcriptomic data highlighted differentially expressed genes. …”
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Transcriptomic and Functional Landscape of Adult Human Spinal Cord NSPCs Compared to iPSC-Derived Neural Progenitor Cells by Sasi Kumar Jagadeesan, Ahmad Galuta, Ryan Vimukthi Sandarage, Eve Chung Tsai

“…RNA sequencing analysis revealed distinct transcriptomic profiles and functional disparities among NSPC types. iPSC-Br NSPCs exhibited a close resemblance to bona fide spinal cord NSPCs, characterized by enriched expression of neurogenesis, axon guidance, synaptic signaling, and voltage-gated calcium channel activity pathways. …”
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Accumulation differences of high-value ingredients in different phenotype Lonicera macranthoides: insights from integrative metabolome and transcriptome analyses by Juan Zeng, Juan Zeng, Yu Qing Long, Yu Qing Long, Jia Yuan Zhu, Jia Yuan Zhu, Xue Sen Fu, Xue Sen Fu, Jing Yu Zhang, Jing Yu Zhang, Jia Wei He, Jia Wei He, Xiao Rong Liu, Xiao Rong Liu, Zhi Hui Wang, Zhi Hui Wang, Qiao Zhen Tong, Qiao Zhen Tong, Xiang Dan Liu, Xiang Dan Liu, Xiang Dan Liu, Ri Bao Zhou, Ri Bao Zhou, Ri Bao Zhou

“…MethodsThe present study intergrated a comparative analysis upon UPLC-MS/MS-based metabolomics and RNA-seq-based transcriptomics to revealed the differences in accumulation of flavonoids, phenolic acids, and terpenoids between the xianglei-type (corolla-closed) and wild-type (corolla-unfolded) of L. macranthoides flowers. …”
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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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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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