Integrating Transcriptomic and Proteomic Data: IL‐27B as a Key Protein in the Development of Septic Cardiomyopathy—A Retrospective Study by Yifeng Mao, Qingqing Chen, Yongpo Jiang, Xijiang Zhang, Qin Si, Panpan Xu, Zhongheng Zhang, Cheng Zheng, Ronghai Lin

“…These findings provide new insights into the pathological mechanisms of SCM and highlight potential therapeutic targets for its treatment. …”
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Investigating the Mechanisms of 15-PGDH Inhibitor SW033291 in Improving Type 2 Diabetes Mellitus: Insights from Metabolomics and Transcriptomics by Yuanfeng Huang, Mingjie Liang, Yiwen Liao, Zirui Ji, Wanfen Lin, Xiangjin Pu, Lexun Wang, Weixuan Wang

“…Then, serum and liver metabolomics, as well as liver transcriptomic analyses, were performed to provide a systematic perspective of the SW033291-ameliorated T2DM. …”
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Transcriptome analysis of hsp18.3 functions and regulatory systems using RNA-sequencing in the red flour beetle, Tribolium castaneum by Wen-feng XIONG, Jia XIE, Lu-ting WEI, Si-si ZHANG, Xiao-wen SONG, Shan-shan GAO, Bin LI

“…Therefore, we compared the global transcriptome profiles of RNA interference (RNAi)-treated larvae (ds-Tchsp18.3) and control larvae of T. castaneum using RNA sequencing. …”
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Meta-analyses of mouse and human prostate single-cell transcriptomes reveal widespread epithelial plasticity in tissue regression, regeneration, and cancer by Luis Aparicio, Laura Crowley, John R. Christin, Caroline J. Laplaca, Hanina Hibshoosh, Raul Rabadan, Michael M. Shen

“…In addition, we have integrated analyses of single-cell transcriptomic states with copy number variants to elucidate transcriptional programs in epithelial cells during human prostate cancer progression. …”
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Exploring the influence of sex and age on the quality and flavor of Huai goat longissimus thoracis et lumborum through transcriptomic and metabolomic analyses by Haoyuan Han, Ziru Kuai, Zhiyun Yao, Xi Lei, Huibin Shi, Jun Li, Kun Liu, Huiru Yin, Yongqing Wang, Kai Quan

“…The identified DEGs and differentially abundant metabolites provide a molecular basis for understanding the variations in meat quality and flavor. …”
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Combined analysis of single-cell and bulk transcriptome sequencing data identifies critical glycolysis genes in idiopathic pulmonary arterial hypertension by Xuan Gao, Youli Fan, Guijia Wang, Jiangjiang Xu, Runwei Deng, Jiangwei Song, Binfeng Sun, Yongbing Wang, Zixuan Wu, Ruyi Jia, Jing Huang, Huiyu He, Lei Gao, Yihao Zhang, Na Sun, Bingxiang Wu

“…Conclusion Our study identifies IGF1, KARS, CASP3, and CDKN2A as key regulatory genes in glycolysis in IPAH, which provides the basis for the development of targeted therapies.…”
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Integrative metagenomic, transcriptomic, and proteomic analysis reveal the microbiota-host interplay in early-stage lung adenocarcinoma among non-smokers by Yaohui Sun, Zhiming Gan, Xiaojin Wang, Jian Liu, Wei Zhong, Zhiyan Zhang, Jiebin Zuo, Hang Zhong, Xiuting Huang, Zhixiang Yan, Qingdong Cao

“…Conclusions Our study depicts the microbial spectrum in patients with ES-LUAD and provides evidence of alterations in lung microbiota and their interplay with the host, enhancing comprehension of the pathogenic mechanisms that underlie ES-LUAD. …”
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Identification of SNPs and Candidate Genes Associated with Growth Using GWAS and Transcriptome Analysis in Portuguese Oyster (<i>Magallana angulata</i>) by Jingyi Xie, Yue Ning, Yi Han, Caiyuan Su, Xiaoyan Zhou, Qisheng Wu, Xiang Guo, Jianfei Qi, Hui Ge, Yizou Ke, Mingyi Cai

“…Differentially expressed genes (DEGs) between individuals with extreme phenotypes were identified using comparative transcriptome analysis, ranging from 868 to 2274 for each trait. …”
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Integrated Transcriptome and Metabolome Analyses Reveal Complex Oxidative Damage Mechanisms in Rice Seedling Roots Under Different Carbonate Stresses by Yang Cao, Fei Hao, Jingpeng Li, Bolun Zhang, Zeming Li, Tiantian Liu, Yan Gao, Xuguang Niu, Xiaohu Liu, Hui Zhang, Lijuan Yang

“…Moreover, the contents of reactive oxygen species (ROS) and malondialdehyde (MDA) were markedly increased, indicating that Na₂CO₃ induces more severe oxidative damage. Transcriptomic and metabolomic analyses revealed a greater number of differentially expressed genes (DEGs) and differentially expressed metabolites (DEMs) in the Na₂CO₃ treatment group. …”
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Clinical potential and experimental validation of prognostic genes in hepatocellular carcinoma revealed by risk modeling utilizing single cell and transcriptome constructs by Hang Deng, Xu Wang, Zi-Ang Jiang, Jian Xu, Yu Zhang, Yao Zhou, Jun Gong, Xiang-Yu Lu, Yi-Fu Hou, Hao Zhang

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Comparative transcriptome analysis of bovine blastocysts reveals specific effects of the oocyte source and the environments during maturation and early embryo development by Mohammad Bozlur Rahman, Eva Held-Hoelker, Mohammed Saeed-Zidane, Franca Rings, Dessie Salilew-Wondim, Dawit Tesfaye, Ahmed Gad, Samuel Gebremedhn, Ernst Tholen, Karl Schellander, Christine Große-Brinkhaus, Michael Hoelker

“…Conclusions The present study provides a comprehensive overview of transcriptomic alterations and pathway disruptions resulting from the in vitro environment following oocyte maturation, offering insight into potential mechanisms underlying embryonic genome activation, DNA duplication and appropriate cell cleavage. …”
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Exploring the Association Between Immune Cell Phenotypes and Osteoporosis Mediated by Inflammatory Cytokines: Insights from GWAS and Single-Cell Transcriptomics by Kuang S, Ma X, Sun L, Wang C, Li Y, Wang G, Sun J, Zhou F, Zhang C

“…Additionally, colo- calization analysis was performed using Bayesian colocalization. Single-cell transcriptomic analysis was performed using datasets from osteoporosis patients available in the Gene Expression Omnibus (GEO) database. …”
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Transcriptomic insights into the interplay between polyketide biosynthesis and other secondary metabolite biosynthetic clusters and biological pathways in entomopathogen Beauveria... by Wachiraporn Toopaang, Wachiraporn Toopaang, Wachiraporn Toopaang, Wachiraporn Toopaang, Thippawan Yoocha, Thippawan Yoocha, Chaiwat Naktang, Chaiwat Naktang, Nuchnudda Wichienchote, Phornsiri Pechsrichuang, Sithichoke Tangphatsornruang, Sithichoke Tangphatsornruang, Morakot Tanticharoen, Yu-Liang Yang, Yu-Liang Yang, Alongkorn Amnuaykanjanasin

“…This regulation pattern suggests that Bbutg1 plays a role in the production or modification of secondary metabolites, specifically during the host infection.ConclusionThis study provides the first transcriptomic evidence that the pks15 cluster regulates multiple secondary metabolite clusters, including bassianolide, siderophores, tenellin, oosporein, and several unidentified PKS and NRPS clusters. …”
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Integration of Network Pharmacology, Transcriptomics, and Metabolomics Strategies to Uncover the Mechanism of Chaihuang Qingfu Pill in Treating Sepsis-Induced Liver Injury by Zhang C, Chen F, Jiang Y, Deng J, Yan X, Yin X, Su B, Liu W

“…Network pharmacological analysis revealed paeoniflorin, quercetin, hyperforin, and wogonin as the core bioactive compounds of CHQF. Transcriptomic profiling identified key targets, including CD14, CXCL2, CCL2, BIRC5, and CXCL8, and demonstrated a significant downregulation of inflammatory cytokines such as TNF-α, IL-6, IL-1β, IL-17, CCL2, CCL3, CCL4, CXCL2, CXCL3, and CXCL5, alongside NF-κB signaling pathway inhibition. …”
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Metabolome and transcriptome analyses reveal the mechanism underlying the differences in skin development between the two duck breeds during embryonic stage by Zhigang Hu, Yingjie Cai, Chang Cao, Hua He, Shun Guo, Na Li, Aiguo Xin, Xiaolin Liu

“…In order to gain a deeper understanding of the genetic factors associated with differences in duck skin color, the transcriptomes and metabolomes of skin between Yulin black duck and Pekin duck from 15 (BSE15 vs. …”
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Single nuclear‐spatial transcriptomic sequencing reveals distinct puncture‐induced cell subpopulations in the intervertebral disc of a rat model by Guoyan Liang, Jing Tan, Chong Chen, Yuying Liu, Yongyu Ye, Xiaolin Pan, Qiujian Zheng, Yunbing Chang, Feng‐Juan Lyu

“…Methods To gain combined spatial and transcriptomic insights into IVDD, we employed both spatial transcriptomic sequencing (stRNA‐seq) and single nucleus RNA sequencing (snRNA‐seq) in a rat puncture‐induced IVDD model. …”
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The Molecular Mechanism and Effects of Root Pruning Treatment on Blueberry Tree Growth by Liwei Chu, Chengjing Shi, Xin Wang, Benyin Li, Siyu Zuo, Qixuan Li, Jiarui Han, Hexin Wang, Xin Lou

“…This study integrated transcriptomics and physiological analyses to elucidate the effects of root pruning on blueberry growth. …”
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A comparison of the large‐scale gene expression patterns in summer and fall migratory Pantala flavescens (Fabricius) in northern China by Lingzhen Cao, Na Wang

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Redefining the high variable genes by optimized LOESS regression with positive ratio by Yue Xie, Zehua Jing, Hailin Pan, Xun Xu, Qi Fang

“…Abstract Background Single-cell RNA sequencing allows for the exploration of transcriptomic features at the individual cell level, but the high dimensionality and sparsity of the data pose substantial challenges for downstream analysis. …”
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siRNA-Silencing of swnR gene greatly reduced biosynthesis of swainsonine in Alternaria oxytropis without affecting the growth characteristics of leguminous host by Yu Zhang, Liwen Yang, Yange Li, Shiyu Tang, Yiqingqing Zhang, Pinzhi Sun, Hao Lu

“…Furthermore, we screened and inoculated a hypovirulent strain suitable for co-cultivation with peeled seed embryos of Oxytropis glabra, and the symbiont showed significantly reduced level of swainsonine without negatively impacting plant growth. These findings provide a promising strategy for mitigating locoism by engineering endophytic fungi with attenuated toxicity.…”
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