Reference-guided detection of the transcriptome reveals circular RNA-related competing endogenous RNA networks in response to three respiration pathogens in pig lungs by Qian Wu, Kun Du, Mao-qing Gu, Yu Xia, Miao Yin, Xian Li, Shu-ting Zhang, Hong Zhao, Zhang-lin Li, Xi-wen Chen

“…Our results identified 72,203 known and 14,344 novel circRNAs and showed that 66, 67, and 197 circRNAs were differentially expressed when lungs were infected by PRRSV, ASFV, and Mhp, respectively. Most differentially expressed circRNAs were up- and down-regulated in response to specific pathogens among PRRSV, ASFV, and Mhp. …”
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Analysis of Transcriptional and Metabolic Differences in the Petal Color Change Response to High-Temperature Stress in Various Chrysanthemum Genotypes by Zhimei Li, Hougao Zhou, Yan Chen, Minyi Chen, Yutong Yao, Honghui Luo, Qing Wu, Fenglan Wang, Yiwei Zhou

“…Flower color is one of the most important ornamental traits of chrysanthemums. …”
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Comparative transcriptomics in B73-teosinte near-isogenic maize lines reveals key defense signaling and phytoalexins in response to Cercospora zeina infection by Xiaomeng Sun, Xiaomeng Sun, Ruiyu Zhang, Ruiyu Zhang, Zongping Wang, Zongping Wang, Haotian Zhang, Haotian Zhang, Hairun Wen, Hairun Wen, Junli Zhang, Naibin Yu, Naibin Yu, Zhe Wang, Zhe Wang, Huanhuan Tai, Huanhuan Tai, Qin Yang, Qin Yang

“…The URGs in Qgls8-R were significantly enriched in metabolic processes, phytohormone signaling, and response to biotic stress, while the URGs in Qgls8-S were mostly involved in plant growth and developmental processes. …”
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The Cholesterol Biosynthesis Pathway Plays an Important Role in Chemotherapeutic Drug Response and Metastasis in High-Grade Osteosarcoma by Amonnat Sukhamwang, Dumnoensun Pruksakorn, Pornngarm Dejkriengkraikul, Apiwat Sangphukieo, Sivamoke Dissook, Supachai Yodkeeree

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Comparative transcriptomic, proteomic, and amino acid content analyses of quinoa (Chenopodium quinoa) seed accessions from diverse geographic locations by María L. Barberini, Yun Sun Lee, Leandro D. Guerrero, Mariana Obertello, María A. Mazzella, Daniel Bertero, Erich Grotewold, Jorge P. Muschietti

“…A Gene Ontology (GO) enrichment analysis of these DEGs showed that the accession representing the NWA transition area was enriched in terms related to oxidative phosphorylation and heat response. Furthermore, using 2D-gel electrophoresis followed by mass spectrometry, we demonstrated that storage proteins, specifically 11S globulin, 13S globulin and vicilin-like antimicrobial peptides, were the most abundant proteins in quinoa seeds of the five accessions. …”
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Transcriptomics and psychotherapy: An integrative review by Itay Ricon-Becker, Steve W. Cole

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Insights of Phaseolus vulgaris’ response to infection by Uromyces appendiculatus using an RNA-seq approach by Penny Makhumbila, Molemi Rauwane, Hangwani Muedi, Sandiswa Figlan

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Identifying Key Biomarkers Related to Immune Response in the Progression of Diabetic Kidney Disease: Mendelian Randomization Combined With Comprehensive Transcriptomics and Single-... by Hu M, Deng Y, Bai Y, Zhang J, Shen X, Shen L, Zhou L

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Association between transcriptomic metrics of exogenous antigen presentation and adaptive immunity with locoregional recurrence in localized estrogen receptor negative breast cance... by Timothy J. Robinson, Casey L. Liveringhouse, Christopher Wilson, Sam Friedman, Justyn Nakashima, Matthew N. Mills, Jacob D. Purcell, Nicholas B. Figura, Du Dongliang, Ram Thapa, Eric Welsh, Kamran A. Ahmed, G. Daniel Grass, Brooke L. Fridley, Roberto Diaz

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Comparative transcriptomic analysis and genome-wide identification provide insights into the potential role of fungal-responsive MAPK cascade genes in tanshinone accumulation in Sa... by Ann Abozeid, Ann Abozeid, Xinru Du, Lan Zhang, Furui Yang, Jianxiong Wu, Lin Zhang, Qi Cui, Zongqi Yang, Dongfeng Yang, Dongfeng Yang

“…Cis-acting element analysis revealed that most SmMAPK genes are associated with stress and phytohormone responses suggesting their involvement in defense mechanisms. …”
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Genome-wide analysis of the CML gene family and its response to cold stress in Curcuma alismatifolia by D. Ying, R. Jintong, W. Yang, F. Zuhong, T. Tian, Z. Hong

“…Transcriptome analysis indicated that CACML140 regulates the cold stress response in Curcuma alismatifolia via the MAPK cascade signaling pathway. …”
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The intensity of the transcriptional response varies across infection with distinct viral strains in an insect host by Allyson M. Ray, Anja Tehel, Jason L. Rasgon, Robert J. Paxton, Christina M. Grozinger

“…While previous research has characterized general host transcriptomic responses to viral exposure, host responses to different DWV strains have not been fully explored. …”
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Transcriptome Analysis of Potato (<i>Solanum tuberosum</i> L.) Seedlings with Varying Resistance Levels Reveals Diverse Molecular Pathways in Early Blight Resistance by Jiangtao Li, Jie Li, Hongfei Shen, Rehemutula Gulimila, Yinghong Jiang, Hui Sun, Yan Wu, Binde Xing, Ruwei Yang, Yi Liu

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Transcriptomic analysis identifies enrichment of cAMP/PKA/CREB signaling in invasive lobular breast cancer by Susrutha Puthanmadhom Narayanan, Abdalla M. Wedn, Osama Shiraz Shah, Jian Chen, Daniel D. Brown, Priscilla F. McAuliffe, Steffi Oesterreich, Adrian V. Lee

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Circadian regulation of the Drosophila astrocyte transcriptome. by Samantha You, Alder M Yu, Mary A Roberts, Ivanna J Joseph, F Rob Jackson

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Diversity of organ-specific plant transcriptomes by Michał Rurek

“…The aim of this review was to summarize the most relevant transcriptomic responses in various plant organs and tissues in the developmental context. …”
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Expression signatures with specificity for type I and II IFN response and relevance for autoimmune diseases and cancer by Bogac Aybey, Benedikt Brors, Eike Staub

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Comprehensive transcriptomic analysis integrating bulk and single-cell RNA-seq with machine learning to identify and validate mitochondrial unfolded protein response biomarkers in... by Lu Zhang, Lei Yue, Peng Jia, Peng Jia, Ziqi Cheng, Jiwen Liu

“…Compared to the sham group, the middle cerebral artery occlusion (MCAO) group exhibited enhanced immune-inflammatory responses. Virtual knockout experiments provide preliminary evidence that CLEC4D functions as a regulatory molecule in neutrophil-mediated inflammation, rather than serving merely as a passive marker.ConclusionCLEC4D was identified as the most sensitive biomarker for IS related to UPRmt-RGs, offering a new reference for IS diagnosis and treatment.…”
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Integrated Transcriptome Analysis Reveals the Lung miRNA–mRNA Regulatory Network Associated with Avian Pathogenic <i>E. coli</i> Infection by Huan Li, Jishuang Tan, Xiaoyi Li, Susan J. Lamont, Hongyan Sun

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Genes highly overexpressed in salt-stressed Young oil palm (Elaeis guineensis) plants by Thalita M. M. Ferreira, André P. Leão, Carlos A. F. de Sousa, Manoel T. Souza Júnior

“…ABSTRACT RNA-seq is a technique based on the large-scale sequencing of transcript-derived cDNAs using next-generation sequencing platforms mostly used today to characterize an organism’s transcriptome. …”
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