Multi-omics whole-genome characterization of the copy number landscape of metastatic pancreatic ductal adenocarcinoma by James T. Topham, Joanna M. Karasinska, Andrew Metcalfe, Hassan A. Ali, Steve E. Kalloger, Maya Kevorkova, Emma Titmuss, Gian Luca Negri, Sandra E. Spencer, Gun Ho Jang, Grainne M. O’Kane, Richard A. Moore, Andrew J. Mungall, Jonathan M. Loree, Faiyaz Notta, Julie M. Wilson, Oliver F. Bathe, Patricia A. Tang, Rachel Goodwin, Gregg B. Morin, Jennifer J. Knox, Steven Gallinger, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, Daniel J. Renouf, David F. Schaeffer

“…Using a multi-omics approach, we integrate whole-genome and transcriptome datasets along with proteomics and clinical metadata to identify copy-altered regions with significant impact on expression at the whole-genome scale. …”
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Genome-wide analyses of the NAC transcription factor gene family in Acer palmatum provide valuable insights into the natural process of leaf senescence by Xin Meng, Chun Feng, Zhu Chen, Faheem Afzal Shah, Yue Zhao, Yuzhi Fei, Hongfei Zhao, Jie Ren

“…In conclusion, this study contributes to elucidating the theoretical foundation of the ApNAC gene family and provides a valuable basis for future investigations into the role of NAC genes in regulating leaf senescence in woody ornamental plants.…”
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Characterization and Expression Profiling of Orphan Genes in Rapeseed (<i>Brassica napus</i>) Provide Insights into Tissue Development and Cold Stress Adaptation by Hong Lang, Yuting Zhang, Baofeng Wang, Kexin Li, Mingliang Jiang

“…The identified expression patterns and structural divergence provide novel insights for breeding stress-resilient varieties.…”
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LAMA4+ CD90+ eCAFs provide immunosuppressive microenvironment for liver cancer through induction of CD8+ T cell senescence by Jianlei Zhang, Zhihui Li, Qiong Zhang, Wen Ma, Weina Fan, Jing Dong, Jingjie Tian, Hongfan Liao, Junzhe Guo, Yabing Cao, Jiang Yin, Guopei Zheng, Nan Li

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Potential Role of CD99 Signaling Pathway in Schwann Cell Dysfunction in Diabetic Foot Ulcers Based on Single-Cell Transcriptome Analysis by Yannan Zhou, Yaxin Zhou, Haohan Chen, Li Zhang, Siwei Bi

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Comprehensive Transcriptome-Wide Profiling of 5-Methylcytosine Modifications in Long Non-Coding RNAs in a Rat Model of Traumatic Brain Injury by Zhijun Xiang, Yixing Luo, Jiangtao Yu, Haoli Ma, Yan Zhao

“…In the present study, we conducted a thorough transcriptome-wide examination of m⁵C methylation in lncRNAs in a rat TBI model utilizing MeRIP-Seq. …”
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Revealing the Response Mechanism of <i>Pediococcus pentosaceus</i> Under Acid and Alcohol Stresses via a Combined Transcriptomic and Metabolomic Analysis by Pan Huang, Huan Yang, Yiyang Zhou, Siyuan Zeng, Rongqing Zhou, Chongde Wu

“…The metabolomic analysis revealed DNA damage under co-stress conditions and further validated the transcriptomic results. Our findings elucidate the molecular and physiological strategies of <i>P. pentosaceus</i> under acid and ethanol stress, providing a foundation for optimizing fermentation processes and enhancing microbial resilience in industrial settings.…”
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Transcriptomic characterisation of acute myeloid leukemia cell lines bearing the same t(9;11) driver mutation reveals different molecular signatures by Elise Georges, William Ho, Miren Urrutia Iturritza, Lel Eory, Kamila Malysz, Ulduz Sobhiafshar, Alan L. Archibald, Daniel J. Macqueen, Barbara Shih, David Garrick, Douglas Vernimmen

“…Conclusion The present study offers a valuable resource by providing a detailed comparative characterisation of the transcriptome of cell lines within the same AML subtype used as models for leukemia research.…”
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LC/MS-based lipidomics and transcriptomics reveal lipid diversity and regulatory networks underlying intramuscular fat differences in Xingguo grey geese by Mengyun Zou, Weihong Zhang, Xiaolan Xiong, Linjie Rao, Qipeng Wei, Haiqin Li, Fanfan Zhang, Jinfang Xie, Zhangzhang Wang, Jiangnan Huang

“…This research emphasizes the significant lipids, genes, and signaling pathways that play roles in IMF accumulation, providing a theoretical basis for enhancing the meat quality of XG geese.…”
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Exploring the association between rheumatoid arthritis and non-small cell lung cancer risk: a transcriptomic and drug target-based analysis by Lyubo Wang, Yuxian Dong, Qingcheng Yang, Siyun Liu, Bencheng Wu, Dahang Zhang, Shuai Shen, Chenjun Xin, Zurui Liu, Qiuyang Wu, Guojian Huang, Lincan Duan

“…Conclusion This study employed transcriptomic analysis and MR of drug targets to elucidate the potential correlation between RA and the risk of developing NSCLC. …”
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Integrated transcriptomic and immune enzymatic analyses uncover coordinated immunometabolic responses in large yellow croaker (Larimichthys crocea) to Metanophrys sp. infection by Ruiling Zhou, Kangshuai Sun, Xiao Xie, Fei Yin, Jorge Galindo-Villegas

“…Together, these findings demonstrate that L. crocea mounts a temporally coordinated immunometabolic response to Metanophrys sp., providing mechanistic insights into mucosal defense and offering candidate biomarkers for targeted disease management in marine aquaculture.…”
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Transcriptomic Profiling of Heat-Treated Oriental Lily Reveals <i>LhERF109</i> as a Positive Regulator of Anthocyanin Accumulation by Mei Zhou, Lijia Zeng, Fan Li, Chunlian Jin, Jungang Zhu, Xue Yong, Mengxi Wu, Beibei Jiang, Yin Jia, Huijuan Yuan, Jihua Wang, Yuanzhi Pan

“…We subjected ‘Souvenir’ Oriental lily plants to temperature treatments (20 °C and 35 °C) and performed transcriptome sequencing and weighted gene co-expression network analysis (WGCNA). …”
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Transcriptomic profiling reveals SARS-CoV-2-infected humanized MHC mice recapitulate human post vaccination immune responses by Siyue Li, Siyue Li, Xuelian Han, Ruolan Hu, Ruolan Hu, Keyu Sun, Min Li, Yuan Wang, Guangyu Zhao, Mengzhe Li, Huahao Fan, Huahao Fan, Huahao Fan, Huahao Fan, Qi Yin

“…Comparative analysis with human whole blood RNA-seq datasets revealed that hMHC mice exhibit both high reproducibility in transcriptomic profiles and significant similarity to human immune responses across innate and adaptive immunity. …”
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Immunologic changes in the peripheral blood transcriptome of individuals with early-stage chronic Chagas cardiomyopathy: a cross-sectional studyResearch in context by Carolina Duque, Jaime So, Yagahira E. Castro-Sesquen, Kelly DeToy, Sneider A. Gutierrez Guarnizo, Fatemeh Jahanbakhsh, Edith Malaga Machaca, Monica Miranda-Schaeubinger, Indira Chakravarti, Virginia Cooper, Mary E. Schmidt, Luigi Adamo, Rachel Marcus, Kawsar R. Talaat, Robert H. Gilman, Monica R. Mugnier

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Integrative Physiological and Transcriptomic Analysis Reveals Metabolic Adaptation and Cold-Tolerance Marker Development in Winter Rye Under Low-Temperature Stress by Haonan Li, Jiahuan Zhao, Chenguang He, Yang Guan, Huimin Guan, Ting He, Dexu Meng, Xiaoping Wang, Yimiao Tang

“…Notably, the KASP-665 marker effectively distinguishes between winter and spring rye, providing a reliable tool for marker-assisted selection in cold tolerance breeding. …”
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Transcriptomic Analysis of Menstrual Blood-Derived Stem Cells Transplantation Combined with Exercise Training in Promoting Spinal Cord Injury Recovery in Rats by QI Longju, CHEN Shiyuan, LIAO Zehua, SHI Yuanhu, SUN Yuyu, WANG Qinghua

“…Spinal cord tissue from the injury site was selected for transcriptome sequencing, and mRNA expression data from both the SCI and CTMT groups were analyzed. …”
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Transcriptomic Analysis Identifies Molecular Response of the Tolerant Alfalfa (<i>Medicago sativa</i>) Cultivar Nongjing 1 to Saline-Alkali Stress by Dongmei Zhang, Jinxia Li, Yiming Zhang, Yuanhao Zhang, Wenhui Wang, Zhaohui Li, Peng Zhu, Yongshun Huang, Long Han, Mingyu Wang, Zijian Zhang, Zhongbao Shen, Weibo Han, Linlin Mou, Xu Zhuang, Qiuying Pang, Jianli Wang, Lixin Li

“…In this study, we conducted transcriptomic analysis on the saline-alkali-tolerant alfalfa cultivar NQ-1 and compared its metabolite accumulation levels with saline-alkali-sensitive cultivars. …”
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Identification of sex determination region and candidate genes in blotched snakehead (Channa maculata) through genome-wide association studies and transcriptome analysis by Haiyang Liu, Tongxin Cui, Jin Zhang, Yang Zhang, Qing Luo, Shuzhan Fei, Kunci Chen, Jian Zhao, Mi Ou

“…Additionally, we performed transcriptome analyses of male and female gonads at 120, 150, and 180 days post-fertilization (dpf). …”
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The comprehensive transcriptomic atlas of porcine immune tissues and the peripheral blood mononuclear cell (PBMC) immune dynamics reveal core immune genes by Qingyao Zhao, Jiahao Wang, Fuping Ma, Quanzhen Chen, Huatao Liu, Jinyan Yang, Siqian Chen, Yongjie Tang, Siyuan Mi, Lulu Wang, Xini Wang, Guohong Liu, Kai Xing, Ying Yu, Chuduan Wang

“…However, comprehensive systematic studies on transcriptome of porcine immune tissues are still rare. …”
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Integrative metabolomics and transcriptomics profiling reveals differential expression of flavonoid synthesis in Ophiopogon japonicus (L. f.) Ker-Gawl. in adaptation to drought. by Tingting Cheng, Juan Lin, Xia Zhou, Hongsu Wang, Xianjian Zhou, Xiaopeng Huang, Tiezhu Chen

“…These findings provide ideas for in-depth analysis of the mechanism of CMD against drought stress, and provide a theoretical basis for breeding high-quality drought-tolerant varieties.…”
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