Differential changes in the microglial transcriptome between neonatal and adult mice after spinal cord injury by Qi Jiang, Shiyuan Xue, Xiaojing Pan, Tengbo Yu, Xinyi Wei, Liping Li, Chao Qi, Weipeng Shi, Zhongkai Ren, Die Hu, Haitao Fu

“…These findings provide valuable insights into potential therapeutic targets for neonatal microglia in the treatment of SCI.…”
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Construction of a prostate adenocarcinoma molecular classification: integrating spatial transcriptomics with retrospective cohort validation by Bingnan Lu, Yifan Liu, Guo Ji, Yuntao Yao, Zhao Yang, Bolin Zhu, Lei Wang, Keqin Dong, Yuanan Li, Jiaying Shi, Junzhe He, Runzhi Huang, Wang Zhou, Xinming Cui, Xiuwu Pan, Xingang Cui

“…Methods Through spatial transcriptome analysis, we identified different malignant cell/spot types in PRAD. …”
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Integrated metabolomic and transcriptomic analysis reveals the biosynthesis mechanism of dihydrochalcones in sweet tea (Lithocarpus litseifolius) by Shaojun Ling, Shaojun Ling, Shaojun Ling, Qiongqiong Lin, Qiongqiong Lin, Qiongqiong Lin, Biaofeng Zhou, Biaofeng Zhou, Biaofeng Zhou, Yiye Liang, Yiye Liang, Yiye Liang, Wenji Luo, Wenji Luo, Wenji Luo, Zhao Shen, Zhao Shen, Zhao Shen, Jingshu Wang, Jingshu Wang, Jingshu Wang, Jingwei Niu, Jingwei Niu, Jingwei Niu, Liangjing Qiao, Liangjing Qiao, Liangjing Qiao, Baosheng Wang, Baosheng Wang, Baosheng Wang, Hui Liu, Hui Liu, Hui Liu

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Transcriptome-wide identification and systematic analysis of the Retrotransposon genes and their roles in ginsenoside biosynthesis in Panax ginseng by Chaofan Wang, Ruicen Liu, Dinghui Wang, Li Li, Yue Jiang, Yanfang Wang, Kangyu Wang, Mingzhu Zhao, Yi Wang, Meiping Zhang

“…Methyl Jasmonate (MeJA)-induced transcriptome analysis identified 15 of 30 genes significantly responsive to MeJA regulation, five of which were strongly linked to ginsenosides contents variation. …”
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Insights into growth retardation and dwarfism caused by goose parvovirus in goslings: a transcriptomic profiling study by Keshan Zhang, Guangliang Gao, Zhuping Chen, Hongyuan Zhang, Xianzhi Zhao, Qin Li, Lin Ma, Lecheng Wang, Yi Luo, Qigui Wang

“…In addition, GPV infection inhibited the proliferation of goose embryo fibroblasts and induced apoptosis, as demonstrated by transcriptomic analysis, which identified 285 differentially expressed genes (DEGs). …”
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Integrating genome and transcriptome analysis to decipher balanced structural variants in unsolved cases of neurodevelopmental disorders by Simona Mellone, Alice Spano, Denise Vurchio, Giulia Borgonovi, Giulia Borgonovi, Alessandro Ugonotti, Giulia Paglino, Alba Bianco, Sara Ronzani, Maurizio Sciancalepore, Flavia Prodam, Flavia Prodam, Amanda Papa, Maurizio Viri, Umberto Dianzani, Umberto Dianzani, Mara Giordano, Mara Giordano

“…RNA sequencing (RNA-Seq), by enabling the detection of gene expression changes and fusion transcripts, provides complementary functional insights into the consequences of genomic alterations. …”
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Physiological and Transcriptomic Mechanisms Underlying Vitamin C-Mediated Cold Stress Tolerance in Grafted Cucumber by Panpan Yu, Junkai Wang, Xuyang Zhang, Zhenglong Weng, Kaisen Huo, Qiuxia Yi, Chenxi Wu, Sunjeet Kumar, Hao Gao, Lin Fu, Yanli Chen, Guopeng Zhu

“…However, 200 mg L⁻¹ treatment elevated malondialdehyde (MDA) content, indicating potential oxidative stress. For transcriptomic analysis, leaves from the 150 mg L⁻¹ Vc and CK treatments were sampled at 0, 1, 2, and 3 days of cold stress. …”
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Multi-omic insights into mitochondrial dysfunction and prostatic disease: evidence from transcriptomics, proteomics, and methylomics by Binbin Gong, Binbin Gong, Binbin Gong, Feixiang Yang, Feixiang Yang, Feixiang Yang, Ning Zhang, Zhengyang Wu, Tianrui Liu, Kun Wang, Xiangyu Zhang, Yangyang Zhang, Zhengyao Song, Chaozhao Liang, Chaozhao Liang, Chaozhao Liang

“…While single-omics studies have provided valuable insights into the role of mitochondrial dysfunction in prostatic diseases, integrating multi-omics approaches is essential for uncovering disease mechanisms and identifying therapeutic targets.MethodsA genome-wide meta-analysis was conducted for prostatic diseases using the genome-wide association studies (GWAS) data from FinnGen and UK Biobank. …”
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Untargeted metabolomics and transcriptomics joint analysis of the effects of polystyrene nanoplastics on lipid metabolism in the mouse liver by Lijuan Chen, Guoyuan Sui, Jin Wu, Ning Li, Zhe Zhang, Ying Du, Meijun Lü, Xiaorui Yan, Guowei Pan, Lianqun Jia

“…The integrated omics data identified dysregulated PC metabolism and CYP gene family expression, suggesting their involvement in arachidonic acid-associated pathways. These findings provided preliminary mechanistic clues linking NP exposure to hepatic lipid metabolism dysregulation and helped to elucidate the adverse effects of NPs on liver lipid metabolism.…”
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Preclinical studies and transcriptome analysis in a model of Parkinson’s disease with dopaminergic ZNF746 expression by Ji Hun Kim, Sumin Yang, Hyojung Kim, Dang-Khoa Vo, Han-Joo Maeng, Areum Jo, Joo-Heon Shin, Joo-Ho Shin, Hyeon-Man Baek, Gum Hwa Lee, Sung-Hyun Kim, Key-Hwan Lim, Valina L. Dawson, Ted M. Dawson, Jae-Yeol Joo, Yunjong Lee

“…Based on this new PD mouse model, we provide unbiased bulk and single-nucleus transcriptomic profiles that are regulated by PARIS and potentially contribute to PD pathogenesis. …”
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An integrated physiological indicator and transcriptomic analysis reveals the response of soybean buds to high-temperature stress by Jiajia Li, Meiyan Wu, Haoran Chen, Wei Liao, Shu Yao, Ying Wei, Heng Wang, Qun Long, Xiaoyu Hu, Wei Wang, Guoji Wang, Lijuan Qiu, Xiaobo Wang

“…Concomitantly, changes in the expression of crucial genes and signal transmission processes are induced, thus initiating adaptive and protective mechanisms. This study provides a theoretical basis for clarification of the physiological and molecular mechanisms in the response to HT stress of soybean bud.…”
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Integrated transcriptomics and metabolomics analysis of flower petals color transition in different phenotype of Lonicera macranthoides by Jiayuan Zhu, Meiling Qu, Juan Zeng, Jiawei He, Jingyu Zhang, Simin Zhou, Qiaozhen Tong, Qiaozhen Tong, Qiaozhen Tong, Qiaozhen Tong, Xiangdan Liu, Xiangdan Liu, Xiangdan Liu, Xiangdan Liu, Xiangdan Liu, Ribao Zhou, Ribao Zhou, Ribao Zhou, Ribao Zhou, Ribao Zhou

“…Genes associated with carotenoid synthesis in the modules identified by KEGG annotation were PSY, PDS, Z-ISO, ZDS, LCYB, BCH, and NXS.ConclusionOur results provide an overall understanding of the regulatory mechanisms underlying differences in petals color transition of different phenotypes of Lonicera macranthoides.…”
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Changes of endogenous hormone concentrations and transcriptome analysis during the healing process of greenwood grafting in grape by DENG Jiayi, WEI Jiayan, CHEN Aisai, HE Fei, YU Keji, WANG Jun

“…[Objective] To study the changes of hormone concentrations in the graft union during the healing process of greenwood grafting, the experiment was carried out, combined with transcriptomic data analysis, so as to identify the key hormone changes in the healing process of greenwood grafting in grape, and provide references for revealing the molecular mechanism of the healing process. …”
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Comparative physiological and cytological analysis, and omics approach provide clues to the coloring mechanism of the pumpkin yellow stems by Liting Deng, Jianning Luo, Haibin Wu, Xiaoxi Liu, Gangjun Zhao, Hao Gong, Xiaoming Zheng, Chaoqun Ni, Xueting Wang, Junxing Li

“…Herein, the physiological, cytological, transcriptome analysis, along with genome-wide association study (GWAS) were integrated to illustrate the processes relevant to pumpkin stem coloring. …”
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Integrated omic analysis provides insights into how Cuscuta australis inhibits the growth and reproduction of Xanthium spinosum by Yunxia Wang, Hubai Bu, Xin Gu, Wanxue Liu, Xinpu Wang

“…Conclusions The results provide a theoretical foundation for the development of targeted pesticides aimed at controlling X. spinosum.…”
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Loss of function of MusaPUB genes in banana can provide enhanced resistance to bacterial wilt disease by Leena Tripathi, Valentine Otang Ntui, Samwel Muiruri, Trushar Shah, Jaindra Nath Tripathi

“…This study identifies MusaPUB22/23 as susceptibility genes and provides strong evidence for their role in modulating immunity in banana. …”
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The single-cell transcription reveals the aberrant differentiation trajectory of chondrocytes in the intervertebral disc for congenital scoliosis by Junfeng Wang, Haodong Li, Dong Fu, Yiming Zheng, Chuang Qian, Lin Li, Maoxiang Qian, Dahui Wang

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A Review of Genomic, Transcriptomic, and Proteomic Applications in Edible Fungi Biology: Current Status and Future Directions by Muyun Xie, Jing Wang, Feixiang Wang, Jinfeng Wang, Yunjin Yan, Kun Feng, Baixiong Chen

“…Understanding the molecular mechanisms governing their growth, development, gene function, biosynthesis of valuable compounds, and environmental adaptation is crucial for enhancing yield and quality, providing essential scientific support for industrial progress. …”
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Dynamic single-cell transcriptomic reveals the cellular heterogeneity and a novel fibroblast subpopulation in laryngotracheal stenosis by Ziwei Liao, Yangyang Zheng, Mingjun Zhang, Xiaoyan Li, Jing Wang, Hongming Xu

“…Conclusions Our study, for the first time, conducted dynamic scRNA-seq on LTS, revealing the cellular heterogeneity and providing a valuable resource for exploring the intricate molecular landscape of LTS. …”
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Deciphering ovarian cancer heterogeneity through spatial transcriptomics, single-cell profiling, and copy number variations. by Songyun Li, Zhuo Wang, Hsien-Da Huang

“…To elucidate the intricate mechanisms underlying HGSOC heterogeneity, we conducted a comprehensive analysis of five single-cell transcriptomes and eight spatial transcriptomes derived from eight HGSOC patients. …”
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