Comprehensive resolution and classification of the Epstein Barr virus transcriptome by Truong D. Nguyen, Jia Wang, Meggie T. Lam, Harris McFerrin, Tina M. O’Grady, Claire Roberts, Nicholas Van Otterloo, Trang T. Nguyen, Melody Baddoo, Dorota Wyczechowska, Maria Morales, Yan Dong, Erik K. Flemington

“…Through long-read sequencing, we provide a comprehensive Epstein Barr virus (EBV) transcriptome analysis, identifying 1453 transcript isoforms and resolving the major isoform of all but one lytic reading frame. …”
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Transcriptome Landscape of Cancer‐Associated Fibroblasts in Human PDAC by Mengyu Tao, Wenting Liu, Jianhua Chen, Rujiao Liu, Jianling Zou, Bo Yu, Chenchen Wang, Mingzhu Huang, Qingjian Chen, Zhe Zhang, Zhiyu Chen, Haoyu Sun, Cheng Zhou, Shuguang Tan, Yuxuan Zheng, Hongxia Wang

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Case Report: FAP+ fibroblasts and SPP1+ macrophages in SMARCA2-deficient while SMARCA4-preserved poorly differentiated lung adenocarcinoma: two case reports and multi-omics analysi... by Zhaoxuan Wang, Junying Wang, Shengmin Wang, Weijiao Xu, Yixiang Zhang

“…Furthermore, we perform a comprehensive multi-omics analysis of the transcriptomic cohort GSE31210 (n=226), the proteomic cohort from the study by Chen et al. …”
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Multiomics-based analysis of the mechanism of ammonia reduction in Sphingomonas by Wang Mingcheng, Wang Mingcheng, Wang Mingcheng, Wang Mingcheng, Liu Daoqi, Xia Huili, Wang Gailing, Liu Chaoying, Guo Yanan, Guo Aizhen, Guo Aizhen, Guo Aizhen

“…To explore the mechanisms of ammonia reduction by Sphingomonas sp. Z392, the transcriptome and metabolome analysis of Sphingomonas sp. …”
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Salidroside ameliorates abnormalities in electrophysiological indices induced by perfusion of the heart with low-potassium solutions by Ruoning Yang, Ruoning Yang, Ruoning Yang, Chi Yan, Chi Yan, Chi Yan, Yifeng Zhou, Yifeng Zhou, Yifeng Zhou, Wenyuan Li, Wenyuan Li, Wenyuan Li, Gongxin Wang, Gongxin Wang, Gongxin Wang, Gongxin Wang, Huan Li, Huan Li, Huan Li, Fei Lin, Fei Lin, Fei Lin, Guoliang Hao, Guoliang Hao, Guoliang Hao, Guoliang Hao

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Integration of Green and Far-Red Light with Red-Blue Light Enhances Shoot Multiplication in Micropropagated Strawberry by Yali Li, Ping Huang, Xia Qiu, Feiyu Zhu, Hongwen Chen, Si Wang, Jiaxian He, Yadan Pang, Hui Ma, Fang Wang

“…Transcriptome analysis identified 144 and 376 differentially expressed genes (DEGs) under RGB and RBFR, respectively, enriched in pathways linked to circadian rhythm, auxin transport, and photosynthesis. …”
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Exploring Differentially Expressed Genes and Immune Modulation in Diffuse Large B-Cell Lymphoma through RNA Sequencing Analysis by Nor Adzimah Johdi, Amanda Seng, Wei-Kang Lee, Hanif Zulkhairi Mohamad Said, Wan Fariza Wan Jamaluddin

“…Background: Diffuse large B-cell lymphoma (DLBCL) is globally recognized as the most prevalent and aggressive subtype of non-Hodgkin lymphoma. While conventional treatments are effective initially, the disease can become resistant or relapse over time. …”
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Identification of functional pathways and hub genes associated with the heterochronic development of sugarcane axillary buds and sett roots through multi-omics analysis by Jiabao Zheng, Xiaoyu Huang, Yanli Wei, Wenyan Li, Baoshan Chen, Baoshan Chen, Wenlan Li, Wenlan Li

“…In addition, we identified differentially expressed genes through transcriptomic analysis and discovered, via GO and KEGG enrichment analyses, that negative regulation of external stimulus response is a key to the preference of ZZ2 for early bud sprouting. …”
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Galangin reduces MPTP-induced dopamine neuron injury via the autophagy dependent-PI3K/AKT pathway by Liping Huang, Liping Huang, Qiaofeng Li, Jingyi Wu, Yingying He, Junwei Huang, Sipeng Xie, Canfeng Yang, Qingling Ruan, Zhongliu Zhou, Minzhen Deng, Minzhen Deng

“…Techniques including network analysis, transcriptomic analysis, rotarod test, enzyme-linked immunosorbent assay (ELISA), qRT-PCR, western blotting, immunohistochemistry, immunofluorescence, and hematoxylin–eosin (HE) were employed to unveil the molecular changes induced by Galangin.ResultsThe network pharmacological analysis showed 301 targets related to Galangin, and 2,858 genes related to PD. …”
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Effects of different shade treatments on the biosynthesis of main phytohormones in the leaves of tea plants by JIN Jing, LÜ Yiqing, HE Weizhong, SHU Zaifa, YE Jianhui, LIANG Yuerong

“…The results showed that blue shade net treatment significantly increased the contents of abscisic acid, gibberellins, auxins, cytokinins, jasmonic acid, and salicylic acid in the tea leaves compared with CK, followed by yellow, black, and red shade net treatments. The transcriptome sequencing results showed that the most abundant number of differentially expressed genes (DEGs) was observed under the black shade net treatment (3 422 up-regulation, and 4 074 down-regulation) compared with CK, subsequently followed by blue shade net treatment (476 up-regulation, and 1 271 down-regulation), and yellow shade net treatment (663 up-regulation, and 994 down-regulation), while the lowest DEGs number was observed under the red shade net treatment (723 up-regulation, and 810 down-regulation). …”
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A comprehensive transcriptional profiling of developing gonads reveals the role of TGFβ signaling in female gonadal asymmetry in chickens by Hong Jo Lee, Jeong Hoon Han, Brittany Chapman, Kyung Min Jung, Isabella Rudd, Jae Yong Han, Tae Hyun Kim

“…In chickens, the left gonad of female embryos develops into a functional ovary, while the right gonad undergoes degeneration during embryogenesis. …”
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Multi-omics joint analysis reveals the mechanism of flower color and fragrance variation in Lilium cernuum by Shaopeng Chen, Zhiqun Chen, Qianqian Zhuang, Hewen Chen

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Deciphering low-dose radiation-induced cytotoxic effects:The application of integrative transcriptomics and metabolomics analysis in lung organoid-based 3D in vitro model by Lihui Xuan, Jinhua Luo, Huiji Pan, Dafei Xie, Xin Huang, Yang Han, Chenjun Bai, Hua Guan, Ruixue Huang, Ping-Kun Zhou

“…Furthermore, these altered lipid metabolites, such as triglycerides and sterols, were enriched in pathways related to cell signaling and affected cell proliferation, differentiation, and death after bioinformatics analysis. Through transcriptomic analysis, compared with the 0 Gy group, the expression of 19 genes in the 0.01 Gy group was up-regulated, while the expression of 6 genes was down-regulated. …”
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Identification and analysis of diverse programmed cell death patterns in idiopathic pulmonary fibrosis using microarray-based transcriptome profiling and single-nucleus RNA sequenc... by Jiazheng Sun, Yulan Zeng

“…IPF-related genes were identified based on differential expression analysis, univariate Cox regression analysis, the “Scissor” program, and the “Findmarkers” program. …”
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Transcriptomic analysis of human primary T cells after short-term leucine-deprivation and evaluation of kinase GCN2's role in regulating differential gene expression. by Aurore Dougé, Gwendal Cueff, Céline Keime, Valérie Carraro, Céline Jousse, Paul Rouzaire, Alain Bruhat

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Integrated transcriptomics and metabolomics analysis reveal the regulatory mechanisms underlying the combined effects of heat and glucose starvation on carotenoid biosynthesis in R... by Xingyu Huang, Caina Guo, Xiaolan Huang, Meixia He, Jingdie Fan, Yuan Chen, Jingwen Qiu, Qi Zhang

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Adaptive Responses of Large Yellow Croaker <i>Larimichthys crocea</i> to Ocean Acidification: Integrative Analysis of Gill and Kidney Transcriptomics and Antioxidant Enzyme Activit... by Ting Ye, Xiaoyan Zhang, Feng Liu, Xiao Liang, Dandan Guo, Bao Lou, Zhigang Xie

“…The lowest MDA content and the highest antioxidant enzyme activities (CAT, SOD, GSH-Px) were observed in <i>L. crocea</i> at pH 7.8, suggesting pH 7.8 was optimal for <i>L. crocea</i>. Transcriptomic analysis revealed distinct gene expression patterns between the gills and kidneys under acidification stress. …”
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Transcriptome analysis reveals potential regulatory mechanism of genes and pathways following Aeromonas veronii infection and hypoxic stress in Chinese mitten crab, Eriocheir sinen... by Gang Jiang, Fengyuan Yan, Yuanfeng Xu, Jianlin Li, Wenrong Feng, Guo an Hua, Wen jing Li, Jun Zhou, Yongkai Tang

“…Moreover, structural damage in hepatopancreas and gills, notably vacuolation and lobular membrane thickening among these treatments. Transcriptome analysis highlighted 157, 135 and 161 differentially expressed genes (DEGs) in treatments Th, Tv, and Thv, respectively, relative to C. …”
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Genetic and transcriptomic analyses of early-onset colon cancer (EOCC): a post hoc analysis of 2973 patients from two adjuvant randomized trials by A. Gandini, C. Gallois, H. Blons, C. Mulot, N. Agueeff, C. Lepage, R. Guimbaud, L. Mineur, J. Desramé, B. Chibaudel, A. de Reyniès, T. André, P. Laurent-Puig, J. Taieb

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Revealing VCAN as a Potential Common Diagnostic Biomarker of Renal Tubules and Glomerulus in Diabetic Kidney Disease Based on Machine Learning, Single-Cell Transcriptome Analysis a... by Li Jiang, Jie Jian, Xulin Sai, Xiai Wu

“…Mendelian randomization analysis confirmed that serum VCAN protein levels were a risky factor for DKD, while there was no reverse association. …”
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