An alteration in the expression of cell wall structural proteins increases cell surface exposure of adhesins to promote virulence in Candida glabrata by Yaling Zhang, Shengwei Gong, Kang Xiong, Xiangtai Yu, Xinreng Mo, Chang Su, Yang Lu

“…Here, we applied RNA sequencing and an in vivo invasive infection model to elucidate the prompt response of C. glabrata during infection. Fungal transcriptomes show a dramatic alteration in the expression of Srp1/Tip1-family cell wall structural proteins during systemic infection. …”
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Tracing the evolutionary pathway of SARS-CoV-2 through RNA sequencing analysis by Mostafa Rezapour, Sean V. Murphy, David A. Ornelles, Patrick M. McNutt, Anthony Atala

“…These findings demonstrate the potential of transcriptomic signatures for variant-agnostic COVID-19 detection and provide a foundation for flexible diagnostic and therapeutic approaches in response to SARS-CoV-2 evolution.…”
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Identification of prognostic long non-coding RNA and construction of competing endogenous RNA networks in pediatric sepsis by LIU Tiantian, ZHAO Yilin, NING Jingjing, ZHANG Yucai, WANG Chunxia

“…The potential targeted microRNAs (miRNAs) and their downstream mRNAs, targeted by the screened lncRNAs, were used to construct a protein-protein interaction (PPI) network and perform pathway enrichment analysis.Results·Transcriptomic data from GSE4607, GSE26440, GSE26378 and GSE9692 revealed 55 differentially expressed lncRNAs associated with prognosis, and miR503 host gene (MIR503HG), TAPT1 antisense RNA 1 (TAPT1-AS1), apoptosis-associated transcript in bladder cancer (AATBC), SBF2 antisense RNA 1 (SBF2-AS1), MGC16275, and small nucleolar RNA host gene 15 (SNHG15) were identified as a 6-lncRNA signature (lncSig6) associated with the prognosis of pediatric septic shock by LASSO regression analysis. …”
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Identification and Mechanistic Studies of Key Genes in Thalamic Hemorrhage Pain by Multi-omics by Chen Yang, Ju Gao, Yaqun Li, Yinggang Xiao, Tianfeng Huang

“…Comprehensive multi-omics profiling involving transcriptomics, proteomics, metabolomics, ribosome profiling (Ribo-seq), and single-cell RNA sequencing (scRNA-seq) was conducted. …”
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Genome-wide identification, characterization, and expression analysis of the MADS-box gene family in grass pea (Lathyrus sativus) under salt stress conditions by Mohamed Abdelsattar, Ahmed E. Nassar, Khaled H. Mousa, Ahmed Hussein, Manal M. S. El-Baghdady, Khaled H. Radwan, Manar S. Ibrahim, Achraf El Allali, Aladdin Hamwieh, Alsamman M. Alsamman, Zakaria Kehel

“…Results In this study, a comprehensive analysis of all MADS-box genes in grass pea was performed at both the genomic and transcriptomic levels. A total of 46 genes were identified and classified based on their MADS-box domains. …”
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Bioinformatics-based prognostic value and in vitro functional validation of PTK6 in cutaneous melanoma by Yanyan Niu, Yanyan Niu, Xiaoyu Liu, Aixiu Shi, Danli Tang, Xiaodong Yao, Yan Lu

“…This study focused on protein tyrosine kinase 6 (PTK6), whose role in CM remains unclear.MethodsTo overcome these limitations, this study focused on PTK6 and integrated CM transcriptomic and clinical data from TCGA and GEO databases. …”
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Hypoxia-induced genome-wide DNA demethylation by DNMT3A and EMT of cancer cells by Biswanath Chatterjee, Pritha Majumder, Chun-Chang Chen, Jing-Ping Wang, Po-Hsuan Su, Hung-Cheng Lai, Ching-Chen Liu, Hsin-Nan Lin, Chen-Hsin A. Yu, Hanna S. Yuan, Che-Kun James Shen

“…Conclusions Altogether, this study has provided the first demonstration of a physiological function of the active DNA demethylation activity of the DNMTs. …”
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Proteomic Analysis Reveals That Dietary Supplementation with Fish Oil Enhances Lipid Metabolism and Improves Antioxidant Capacity in the Liver of Female <i>Scatophagus argus</i> by Jingwei He, He Ma, Dongneng Jiang, Tuo Wang, Zhiyuan Li, Gang Shi, Yucong Hong, Chunhua Zhu, Guangli Li

“…These proteomic findings align with prior transcriptomic data, indicating that dietary fish oil enhances hepatic lipid metabolism, mitigates oxidative stress, and strengthens antioxidant capacity. …”
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KSHV reprograms host RNA splicing via FAM50A to activate STAT3 and drive oncogenic cellular transformation by Shenyu Sun, Ling Ding, Karla Paniagua, Xian Wang, Yufei Huang, Mario A. Flores, Shou-Jiang Gao

“…To elucidate the mechanisms by which KSHV-driven splicing reprogramming mediates cellular transformation, we performed transcriptomic sequencing, identifying 131 differentially alternative spliced transcripts, with exon skipping as the predominant event. …”
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Virus-specific host responses and gene signatures following infection with major SARS-CoV-2 variants of concern: role of ZBP1 in viral clearance and lung inflammation by Amany Elsharkawy, Amany Elsharkawy, Hamid Reza Jahantigh, Anchala Guglani, Shannon Stone, Komal Arora, Mukesh Kumar, Mukesh Kumar

“…Herein, using RNA sequencing, we performed a comparative transcriptomic analysis following infection with major VOCs. …”
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Characterization of lysine crotonylation-related lncRNAs for prognostic assessment and immune response in glioma by Miaomiao Song, Juan Xu, Zhonghao Gui, Yun Wu, Feifei Wang, Hongmei Sheng, Xueyong Huang, Junyu Qian, Haotian Qin, Ying Wang, Ying Wang

“…The LCRlncRNA-based risk model provides a promising tool for prognostic evaluation and personalized therapy design in glioma.…”
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p53 and TIGAR promote redox control to protect against metabolic dysfunction-associated steatohepatitis by Celine I. Wittke, Eric C. Cheung, Dimitris Athineos, Nicola Clements, Liam Butler, Mark Hughes, Vivienne Morrison, Dale M. Watt, Karen Blyth, Karen H. Vousden, Timothy J. Humpton

“…Human relevance is examined through transcriptomic analyses of patients with MASH. Results: Using a p53 reporter mouse, we report early and sustained activation of hepatic p53 in response to a high-fat and high-sugar diet (p <0.05 at 100 days in males, p <0.001 at 200 days in females). …”
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Temporal GeneTerrain: advancing precision medicine through dynamic gene expression visualization by Ehsan Saghapour, Ehsan Saghapour, Rahul Sharma, Delower Hossain, Delower Hossain, Kevin Song, Kevin Song, Zhandos Sembay, Zhandos Sembay, Jake Y. Chen, Jake Y. Chen

“…We applied Temporal GeneTerrain to compare transcriptomic perturbations induced by mefloquine (M), tamoxifen (T), and withaferin A (W), both individually and in all-pairwise and triple combinations (TM, TW, MW, and TMW), in LNCaP prostate cancer cells using the GSE149428 dataset (0, 3, 6, 9, 12, and 24 h). …”
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Heat stress-induced genomic instability in neural stem cells and its association with neuronal developmental deficits by Zeze Wang, Zhen Luo, Yulong Tan, Xue Luo, Xuesen Yang

“…We employed a multi-omics approach to assess the consequences, including high-content neuromorphometrics, strand-specific RNA sequencing (RNA-seq) for transcriptomic and genomic variant analysis, and immunofluorescence for DNA double-strand breaks (DSBs) using the γH2AX marker. …”
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Isodon lophanthoides alleviates liver fibrosis via modulation of purine metabolism and NF-κB signaling pathway: insights from multi-omics analysis by Kuikui Chen, Kuikui Chen, Kuikui Chen, Jie Liang, Jie Liang, Yong Tan, Yong Tan, Yaohua Li, Xiaojiao Pan, Xiaojiao Pan, Zhonghui Guo, Zhonghui Guo, Wentao Zhang, Zongxi Sun

“…An integrated multi-omics approach encompassing transcriptomics, proteomics, and metabolomics was used to elucidate the underlying mechanisms, further supported by Western blotting, targeted metabolite quantification, and enzyme-linked immunosorbent assay (ELISA).ResultsThirty-two metabolites were identified in ILW. …”
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Regulatory effects of the bidirectional crosstalk between hepatic gene expressions and gut microbiota on the productive performances and egg quality of induced molting treated laye... by Fuguang Xue, Pengyun Ma, Yunlei Li, Xiaoke Zhang, Xinying Xu, Zhong Ma, Yanyan Sun, Jingwei Yuan, Hui Ma, Jinsong Pi, Huadong Wu, Ling Li, Yuanqi Qu, Jilan Chen

“…Productive performances and egg quality were meticulously recorded for each replicate, followed by the sampling of one bird from each replicate for the intestinal morphological analysis. The16S rRNA and transcriptomic sequencing methods were conducted for microbial communities and hepatic gene expressions investigation between CON and FM treatments to investigate the potential regulatory effects on productive performances and egg quality. …”
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An adoptive cell therapy with TREM2‐overexpressing macrophages mitigates the transition from acute kidney injury to chronic kidney disease by Yating Zhang, Yu Liu, Siweier Luo, Hanzhi Liang, Chipeng Guo, Yufei Du, Hongyu Li, Le Wang, Xiaohua Wang, Chun Tang, Yiming Zhou

“…RNA‐seq was used to investigate transcriptomic changes between WT and Trem2 knockout bone marrow‐derived macrophages (BMDMs). …”
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Tricin selectively combats KRAS-mutant non-small cell lung cancer by inhibiting the PDGF-BB-induced SRC/MAPK/AP-1/PD-L1 signaling pathway and potentiating the antitumor effect of a... by Jia-Xin Li, Jia-Xin Li, Shi-Yu Tan, Li-Qi Li, Yu-Hong Zheng, Lin Zhao, Hui-Rong Zhu, Hai-Lang He, Yan-Yu Zhang, Run-Ze Li, Tian-Yu Bao, Yi-Zhong Zhang, Xiao-Man Yang, Hao Zhang, Hui-Hui Chen, Bo-Wen Wu, Xin Lin, Xiao-Sheng Lin, Xiao-Sheng Lin, Yin Cheng Lin, Xin-Bing Sui, Ying Xie, Xian-Mei Zhou, Pei-Yu Yan

“…Next, we integrated network pharmacology, molecular docking with transcriptomics analysis and biological methods to probe the underlying mechanisms of tricin in the treatment of patients with KRAS-mutant NSCLC. …”
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Maternal intestinal L. vaginalis facilitates embryo implantation and survival through enhancing uterine receptivity in sows by Qianhong Ye, Yifan Hu, Haoyi Jiang, Tingting Luo, Longshan Han, Yuwen Chen, Jiaying Chen, Libao Ma, Ziyi He, Xianghua Yan

“…We further employed transcriptomic analysis to determine the characteristics of uterus, which found an enhanced uterine receptivity after L. vaginalis gavage. …”
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Nervonic acid triggered ovarian inflammation by inducing mitochondrial oxidative stress to activate NLRP3/ IL-1β pathway by Xiangzhou Zeng, Xinyin Fan, Haitao Yu, Shuang Cai, Liangrui Zhou, Huanwen Wu, Zhiwen Zhang, Shuang Quan, Siyu Li, Xinyu Wang, Bangxin Xue, Lu Liu, Shiyan Qiao, Xiangfang Zeng

“…Through biological techniques such as transcriptomics, CUT&Tag, and analysis of post-translational protein modifications, the molecular mechanisms underlying NA mediated ovarian inflammation were further elucidated based on models utilizing ovarian granulosa cells from pigs, humans, and mice. …”
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