Transcriptomic analysis reveals vector attraction to potato virus Y is mediated through temporal regulation of TERPENE SYNTHASE 1 (TPS1) by Chad T. Nihranz, Prakriti Garg, Junha Shin, Madeleine Dumas, Sunnie Grace McCalla, Sushmita Roy, Clare L. Casteel

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Single-cell sequencing and transcriptomic data reveal that P65 activation significantly promotes microglia-mediated neuroinflammation after ischemic stroke by Ruiyu Wang, Yilun Qian, Xinchen Zhou, Hang Xu, Yu Wang, Yao Geng, Tianshu Wang, Binxiu Sha

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Integrative transcriptomic and proteomic analyses reveal that carbon metabolism and complement system of Madin Darby Bovine Kidney cells are affected by bovine coronavirus infectio... by Hui Zhang, Qisheng Yu, Rui Guo, Qing Zhu, Jin Yu, Zhaohui Zhang, Lan Lan, Cheng Tang, Changqing Yu, Bin Zhang

“…Following GO annotation and KEGG enrichment analysis, most DEGs and DEPs were significantly enriched in metabolic pathways, endocytosis, ribosome and protein processing in endoplasmic reticulum, apoptosis and immune response. A correlation analysis of the proteome and transcriptome revealed that the up-regulated DEGs and DEPs were predominantly associated with metabolic pathways, apoptosis and the MAPK/TNF/Ras signaling pathway, whereas the down-regulated DEGs and DEPs were involved in complement and coagulation cascades and the Wnt signaling pathway. …”
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Genome-Wide Transcriptome Analysis Reveals GRF Transcription Factors Involved in Methyl Jasmonate-Induced Flavonoid Biosynthesis in <i>Hedera helix</i> by Feixiong Zheng, Zhangting Xu, Xiaoji Deng, Xiaoyuan Wang, Yiming Sun, Xiaoxia Shen, Zhenming Yu

“…In the present study, the flavonoid content was significantly increased after MeJA treatment and peaked at 6 h post-treatment. A total of 31,931 genes were identified using transcriptome, and 6484 DEGs were identified at 6 h post-treatment. …”
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Single-cell transcriptomic analysis identifies systemic immunosuppressive myeloid cells and local monocytes/macrophages as key regulators in polytrauma-induced immune dysregulation by Drishti Maniar, M. Cole Keenum, Casey E. Vantucci, Tyler Guyer, Paramita Chatterjee, Kelly Leguineche, Kaitlyn Cheung, Robert E. Guldberg, Krishnendu Roy

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Identifying key palmitoylation-associated genes in endometriosis through genomic data analysis by Jinyan Kai, Jiaqi Su, Yinping You, Xiaoliang Liang, Haitao Huang, Jie Fang, Qiong Chen

“…Abstract Background Palmitoylation, a post-translational lipid modification, has garnered increasing attention for its role in inflammatory processes and tumorigenesis. …”
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Transcriptomics and non-targeted metabolomics provide mechanistic insights into the improvement of the growth performance and meat quality of lambs supplemented with fermented Lyci... by Jiale Liao, Wencan Ke, Bing Wang, Min Du, Qiang Lu, Yajun Zhang, Guijie Zhang

“…The underlying mechanisms responsible for the beneficial effect of LBR and FLBR on the longissimus thoracis (LT) and intramuscular fat (IMF) tissues of lambs were examined using multiomics techniques. …”
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Standardised Forms of Chondroitin Sulfate as a Pathogenetic Treatment of Osteoarthritis in the Context of Post-Genomic Studies by O. A. Gromova, I. Yu. Torshin, A. M. Lila, L. I. Alekseeva, E. A. Taskina

“…A systematic analysis of 37 post-genomic osteoarthritis (OA) studies (genomics, transcriptomics, proteomics, metabolomics) allowed to isolate 483 genes and corresponding proteins, their levels and activity disturbances are involved in the pathogenesis of the disease. …”
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A multi-omic approach implicates novel protein dysregulation in post-traumatic stress disorder by Jiawei Wang, Yujing Liu, Hongyu Li, Tuan P. Nguyen, John Lee Soto-Vargas, Rashaun Wilson, Weiwei Wang, TuKiet T. Lam, Chi Zhang, Chen Lin, Traumatic Stress Brain Research Group, David A. Lewis, Jill Glausier, Paul E. Holtzheimer, Matthew J. Friedman, Kenneth R. Williams, Marina R. Picciotto, Angus C. Nairn, John H. Krystal, Ronald S. Duman, Keith A. Young, Hongyu Zhao, Matthew J. Girgenti

“…Integrative analysis with transcriptomics and miRNA data from the same cohort pointed to hsa-mir-589 as a regulatory miRNA responsible for dysregulation of neuronal protein networks for PTSD, including the gamma-aminobutyric acid (GABA) vesicular transporter, SLC32A1. …”
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Interaction between post-tumor inflammation and vascular smooth muscle cell dysfunction in sepsis-induced cardiomyopathy by Rui Liu, Lina Jia, Lin Yu, Detian Lai, Qingzhu Li, Bingyu Zhang, Enwei Guo, Kailiang Xu, Qiancheng Luo

“…This study aims to elucidate the interaction between post-tumor inflammation, intratumor heterogeneity, and the dysfunction of VSMC in SIC, as well as to evaluate the therapeutic potential of exercise training and specific pharmacological interventions.MethodsTranscriptomic data from NCBI and GEO databases were analyzed to identify differentially expressed genes (DEGs) associated with SIC. …”
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Redefining the role of IL-18 in post-surgical recovery and sepsis: a key mediator of inflammation resolution by Ioanna Papatheodorou, Gabriela Blažková, Veronika Bosáková, Zuzana Tomášiková, Erin Spearing, Robin Klieber, Pavel Ostašov, Julie Štíchová, Martina Dvončová, Alexandra Mýtniková, Jan Emmer, Kamila Bendíčková, Tomáš Tomáš, Vladimír Šrámek, Petros Kolovos, Monika Holubová, Martin Helán, Marcela Vlková, Jan Frič, Marcela Hortová-Kohoutková

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Roles of P-body factors in Candida albicans filamentation and stress response. by Melissa A Tosiano, Frederick Lanni, Aaron P Mitchell, C Joel McManus

“…These results support a model in which DHH1, but not EDC3, represses hyphal stress response transcripts in yeast and remodels the transcriptome during filamentation. …”
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Novel insights into post-myocardial infarction cardiac remodeling through algorithmic detection of cell-type composition shifts. by Brian Gural, Logan Kirkland, Abigail Hockett, Peyton Sandroni, Jiandong Zhang, Manuel Rosa-Garrido, Samantha K Swift, Douglas J Chapski, Michael A Flinn, Caitlin C O'Meara, Thomas M Vondriska, Michaela Patterson, Brian C Jensen, Christoph D Rau

“…Interpreting bulk RNA sequencing from heterogeneous tissues like the post-myocardial infarction (MI) heart is confounded by dynamic changes in cell-type composition. …”
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Prioritizing perturbation-responsive gene patterns using interpretable deep learning by Yan Cui, Zhiyuan Yuan

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Metabolome integrated with transcriptome, and genome analysis revealed higher accumulations of phytoalexins enhance resistance against Magnaporthe oryzae in new Zhefang rice variet... by Owais Iqbal, Xingrun Yang, Ruoping Wang, Chun Wang, Dandan Li, Jiancheng Wen, Jiasheng Ding, Sauban Musa Jibril, Chengyun Li, Yi Wang

“…Results This study employed an integrated metabolomic, transcriptomic, and genomic approach to compare the response of Diantun susceptible (D502) and resistant (D506) rice lines to M. oryzae infection at 48 h post-inoculation. …”
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Senescence-associated alterations in histone H3 modifications, HP1 alpha levels and distribution, and in the transcriptome of vascular smooth muscle cells in different types of sen... by Agnieszka Gadecka, Marta Koblowska, Helena Kossowska, Roksana Iwanicka-Nowicka, Dorota Janiszewska, Grażyna Mosieniak, Krzysztof Bojakowski, Krzysztof Goryca, Anna Bielak-Zmijewska

“…Methods We investigated the level and distribution of HP1α and H3 modifications that are markers of hetero- and euchromatin (H3K9me3, H3K27me3, H3K4me3, H3K9Ac - WB and IF), alterations in the transcriptomic profile (DNA microarray, qPCR), H3K4me3, H3K9me3 and HP1α protein distribution in the genome (ChIP-seq), and expression of enzymes involved in histone post-translational modifications (DNA microarray, qPCR, WB, IF). …”
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Genome-Wide Responses of Female Fruit Flies Subjected to Divergent Mating Regimes. by Dave T Gerrard, Claudia Fricke, Dominic A Edward, Dylan R Edwards, Tracey Chapman

“…Preliminary experimental manipulation of two genes in that network with roles in post-transcriptional modification (CG11486, eyegone) tended to enhance sensitivity to mating costs. …”
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Transcriptome and Physio-Biochemical Profiling Reveals Differentially Expressed Genes in Seedlings from Aerial and Subterranean Seeds Subjected to Drought Stress in <i>Amphicarpaea... by Jiancheng Kou, Yue Su, Tianyu Lei, Siqi Hou, Jiali Tian, Minglong Li, Shuzhen Zhang, Xiaodong Ding, Qiang Li, Jialei Xiao

“…We identified 1317 and 2029 differentially expressed genes (DEGs) in AS seedlings five and ten days post-drought treatment, respectively, and 1793 DEGs in SS seedlings ten days post-drought treatment compared to the normal treatment (CK). …”
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Exploring the molecular mechanism of OsROS1a in regulating resistance to bacterial leaf streak through transcriptome and DNA methylation profiling in rice (Oryza sativa L.) by Xiaofang Xie, Xuansong Yang, Libin Lu, Tong Li, Mingyue Qin, Huazhong Guan, Yan Zheng, Tao Lan, Weiren Wu

“…Using whole-genome bisulfite sequencing (WGBS) and RNA-sequencing (RNA-seq), we analyzed the DNA methylations and transcriptomes of RS lines in comparison with NP at 0 (control), 5, 10, and 24 h post-inoculation with Xoc. …”
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Blocking Tim-3 enhances CD8+ T cell activity to inhibit hepatocellular carcinoma recurrence post-radiofrequency ablation by Na Wu, Xinru Pei, Weiguo Cai, Xiaodie Ye, Wei Lu

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