Identification of long noncoding RNAs (lncRNAs) and co-transcriptional analysis of mRNAs and lncRNAs in transcriptomes of Anopheles gambiae by Jiannong Xu, Kai Hu, Michelle M. Riehle, Vedbar S. Khadka

“…While it is widely appreciated that long non-coding RNAs (lncRNAs) are expressed ubiquitously in transcriptomes across metazoans, lncRNAs remain relatively underexplored in An. gambiae, including their identity, expression profiles, and biological functions. …”
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Liver Transcriptome Analysis Reveals a Potential Mechanism of Heat Stress Increasing Susceptibility to <i>Salmonella</i> Typhimurium in Chickens by Qi Zhang, Yvqing Zhu, Zixuan Wang, Qinghe Li, Guiping Zhao, Qiao Wang

“…Combined differential expression analysis and WGCNA identified three hub regulatory genes: <i>PTGDS</i> and <i>WISP2</i> showed significant correlations with the heterophil/lymphocyte ratio, while <i>SLC6A9</i> was significantly correlated with serum IL-8 levels. …”
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Decoding the striatum of drug-naive patients with obsessive-compulsive disorder: a transcriptome and longitudinal functional magnetic resonance imaging study by Yiding Han, Haohao Yan, Xiaoxiao Shan, Huabing Li, Feng Liu, Ping Li, Dongsheng Lv, Jingping Zhao, Wenbin Guo

“…Furthermore, integrating transcriptomic and rs-fMRI findings offer novel insights into the biological substrates underlying the altered EC of SSs in OCD patients.…”
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Red Blood Cell Transcriptome Reflects Physiological Responses to Alternative Nutrient Sources in Gilthead Seabream (<i>Sparus aurata</i>) by Rafael Angelakopoulos, Andreas Tsipourlianos, Alexia E. Fytsili, Leonidas Papaharisis, Arkadios Dimitroglou, Dimitrios Barkas, Zissis Mamuris, Themistoklis Giannoulis, Katerina A. Moutou

“…The downregulation of oxidative phosphorylation genes suggests a metabolic shift in response to altered nutrient composition, while ribosomal pathway modulation indicates potential constraints on protein synthesis. …”
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Integrated physiological and transcriptomic analyses reveal the mechanism of reduction in wheat fertile floret number under spring low-temperature stress by Ying Weng, Zhiwei Tang, Weixiang Huang, Rui Wang, Feifei Wang, Hongmei Cai, Hao Wang, Zehao Liu, Baoqiang Zheng, Jincai Li, Xiang Chen

“…At 0–15 d after low-temperature stress (DALTS), SLTS caused a brief increase in the sugar content of young spikes (0–3 DALTS), followed by a rapid decrease (6–15 DALTS), while the total nitrogen content keeps decreasing. …”
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48-Hour and 24-Hour Time-lapse Single-nucleus Transcriptomics Reveal Cell-type specific Circadian Rhythms in Arabidopsis by Yuwei Qin, Zhijian Liu, Shiqi Gao, Carlos Martínez-Vasallo, Yanping Long, Xinlong Zhu, Bin Liu, Ya Gao, Xiaodong Xu, Maria A. Nohales, Qiguang Xie, Jixian Zhai

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Cesium Accumulation Patterns and Stress Response in Hydroponic Radish (<i>Raphanus sativus</i> L.): A Physiological–Transcriptomic Study by Yu-Han Wen, Xi Chen, Ming Sun, Chao-Hui Yang, Meng-Yuan Xu, Feng-Xiang Lai, Si-Qi Fu, Yu-Meng Fan, Xin-Peng Guo, Qun Li, Guo Wu

“…The transfer factor (TF) increased by 63.29% (TF = 3.87) as the Cs concentration increased from 0.25 to 2 mM, while the biological concentration factor (BCF) decreased by 72.56% (BCF = 14.87). …”
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Transcriptomic Differences by RNA Sequencing for Evaluation of New Method for Long-Time In Vitro Culture of Cryopreserved Testicular Tissue for Oncologic Patients by Cheng Pei, Plamen Todorov, Qingduo Kong, Mengyang Cao, Evgenia Isachenko, Gohar Rahimi, Frank Nawroth, Nina Mallmann-Gottschalk, Wensheng Liu, Volodimir Isachenko

“…In this comparison, significantly up-regulated genes included C4B_2, LOC107987373, and GJA4, while significantly down-regulated genes included SULT1A4, FBLN2, and CCN2. …”
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Pharmacological Effects of Antioxidant Mycosporine-Glycine in Alleviating Ultraviolet B-Induced Skin Photodamage: Insights from Metabolomic and Transcriptomic Analyses by Kai Wang, Ling Qin, Huan Lin, Mengke Yao, Junhan Cao, Qing Zhang, Changfeng Qu, Yingying He, Jinlai Miao, Ming Liu

“…M-Gly treatment improved skin appearance and reduced mast cell numbers, while also elevating antioxidant levels, including superoxide dismutase (SOD), catalase (CAT), and glutathione (GSH). …”
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Decoding submergence tolerance in Prunus persica: Integrated transcriptomic and metabolomic acclimations of antioxidant system, cell wall dynamics, and hormonal signaling by Muhammad Ateeq, Dongmei Zhang, Jinping Xiao, Huiqin Zhang, Xingyi Shen, Jian Meng, Jinzhi Yang, Shariq Mahmood Alam, Muhammad Mohsin Kaleem, Muhammad Abbas Khan, Kaijie Zhu, Guohuai Li, Junwei Liu

“…Abstract Low oxygen stress (hypoxia) induced by submergence significantly impairs respiration in fruit trees, leading to reduced yield and, in extreme cases, tree mortality. While extensive research has focused on the root responses of peach trees to waterlogging, the mechanisms underlying leaf responses to complete submergence remain poorly understood. …”
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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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Comparative transcriptome analysis provides a glance into the regulation of the Krüppel homolog 1 on the reproduction and diapause of the predatory ladybeetle, Coccinella septempun... by Junjie Chen, Xiaoxiao Liu, Shunda Han, Maosen Zhang, Zhaohan Liu, Yuyan Li, Lisheng Zhang

“…In this study, we utilized RNA-Sequencing to investigate the transcriptomic changes in C. septempunctata following RNA interference targeting the Kr-h1 gene. …”
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Microscopical Observation and Transcriptome Analysis Reveal the Effects of High‐Altitude Ecosystem in the Qualities of Different Genetic Varieties Brassica napus Resources by Zongji Zhang, Xionghua Li, Ri Ming, Yingying Lu, Qinwen Lin, Yafei Yang, Jialin Liao, Yunjuan Li, Lingli Mao, Yang Huang, Li Zhong, Yu Liang

“…The soluble sugar and cellulose contents of some varieties decreased, while ascorbic acid and protein increased by 74% and 85%, respectively. …”
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Claroideglomus etunicatum enhances Pteris vittata L. arsenic resistance and accumulation by mediating the rapid reduction and transport of arsenic in roots by Guofei Pan, YueZhen Xu, WeiZhen Li, Linyan Zan, Xueli Wang

“…C. etunicatum enhances arsenic uptake by mediating the MIP, PHT, and NRT transporter families, while also increasing arsenic reduction (PvACR2 direct reduction and vesicular PvGSTF1 reduction). …”
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Integrated metabolomic, transcriptomic and network analysis elucidates therapeutic mechanisms of Ganoderma lucidum spore oil against granulomatous pulmonary nodules by Ya Liu, Wendong Xu, Kexin Wang, Kexin Wang, Zhiye You, Xiaohong Chen, Xiaohong Chen, Huihui Ti, Xiaoli Liang, Lin Cao, Hongfei Cai, Juyan Liu, Zifeng Yang, Zifeng Yang, Zifeng Yang

“…Results revealed that GLSO markedly reduced granuloma area and ground glass opacities in the lungs while attenuating pulmonary inflammation and chemokine levels. …”
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Probiotic Bacillus pumilus LV149 enhances gut repair, modulates microbiota, and alters transcriptome in DSS-induced colitis mice by Xinyu Sun, Long Yun, Keming Xie, Renhui Liu, Xinyue Ren, Bokun Zeng, Xudong Cao, Zhi Li, Guihao Zhou, Bang Liu, Luo Peng, Lihong Yuan

“…Notably, only the LV149-H significantly decreased the expression of pro-inflammatory cytokines TNF-α, IL-1β, and IL-6, while both doses increased the expression of the anti-inflammatory cytokine IL-10 in a dose-dependent in colonic tissue. …”
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Copper Pyrithione Induces Hepatopancreatic Apoptosis and Metabolic Disruption in <i>Litopenaeus vannamei</i>: Integrated Transcriptomic, Metabolomic, and Histopathological Analysis by Jieyu Guo, Yang Yang, Siying Yu, Cairui Jiang, Xianbin Su, Yongfeng Zou, Hui Guo

“…Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of metabolomics and transcriptome revealed that both DEGs and SDMs were enriched in arachidonic acid metabolism, fatty acid biosynthesis, and glycolysis/gluconeogenesis pathways at 3 h, while at 48 h they were enriched in the starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism, and galactose metabolism pathways. …”
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Physiological, transcriptomic and metabolomic analyses reveal the mechanism of CuO and silicon nanoparticles involved in Polygonatum kingianum response to root rot by Xi Xu, Jinpeng Wan, Guizhou Liu, Chengkai Lu, Xinyu Mao, Jinglin Wu, Hanying Liu, Yong Ding, Peng Xu

“…A Pearson coefficient analysis showed that 22 genes were positively correlated with the disease index under CuNP treatment, while 27 genes were positively correlated under SiNP treatment. …”
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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

“…The pharmacological mechanisms of CHQF were explored using network pharmacology, transcriptomics, and metabolomics, which enabled the identification of potential therapeutic targets and pathways, as further validated by in vivo and in vitro experiments.Results: CHQF administration significantly improved the survival rates, reduced systemic inflammation, and restored liver function in CLP-induced sepsis mice, while also mitigating liver tissue injury. …”
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