Transcriptomic analyses implicate neuronal plasticity and chloride homeostasis in ivermectin resistance and response to treatment in a parasitic nematode. by Roz Laing, Stephen R Doyle, Jennifer McIntyre, Kirsty Maitland, Alison Morrison, David J Bartley, Ray Kaplan, Umer Chaudhry, Neil Sargison, Andy Tait, James A Cotton, Collette Britton, Eileen Devaney

“…Overall, we show the utility of a genetic cross to identify differences in gene expression that are specific to ivermectin selection and provide a framework to better understand ivermectin resistance and response to treatment in parasitic helminths.…”
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Metabolome and transcriptome analyses reveal molecular responses of two potato (Solanum tuberosum L.) cultivars to cold stress by Xiang Li, Xiang Li, Xiang Li, Zhenzhen Zheng, Yun Zhou, Yun Zhou, Yun Zhou, Shenglong Yang, Shenglong Yang, Shenglong Yang, Wang Su, Wang Su, Wang Su, Heng Guo, Heng Guo, Heng Guo, Guangji Ye, Guangji Ye, Guangji Ye, Jian Wang, Jian Wang, Jian Wang

“…DiscussionOur results provided novel insights into the molecular mechanisms underlying cold resistance in potato.…”
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Lipidomics and Transcriptomics Analyses Reveal Dietary Complex Plant Extracts Improve Lipid Composition of Back Fat in Sheep by Hui Guo, Ruixue Nie, Tao Guo, Chang Gao, Jinju Mao, Yuchao Hu, Wenwen Wang, Na Liu, Xiaoping An, Jingwei Qi, Yuan Wang

“…This study aimed to examine the effect of dietary CPE supplementation on sheep growth performance and fatty acid composition in back fat (BF), combining lipidomics and transcriptomics analyses to explain the underlying mechanisms. …”
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Hepatotoxicity in Carp (<i>Carassius auratus</i>) Exposed to Perfluorooctane Sulfonate (PFOS): Integrative Histopathology and Transcriptomics Analysis by Lin Tang, Guijie Hao, Dongren Zhou, Yunpeng Fan, Zihao Wei, Dongsheng Li, Yafang Shen, Haoyu Fang, Feng Lin, Meirong Zhao, Haiqi Zhang

“…Histopathological and transcriptomic analyses confirmed PFOS-induced liver damage in the carp, characterized by venous congestion, nucleolar dissolution and cellular vacuolation. …”
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Integrated single-cell transcriptome and TCR profiles of hepatocellular carcinoma highlight the convergence on interferon signaling during immunotherapy by Xiaobo Li, Chang Xu, Mingjie Zhang, Shengnan Guo, Dapeng Hao, Changqing Liu, Jing Ren, Guangyu Wang, Cheng Lyu, Tianhao Li, Huanhuan Xu, Zepeng Hou, Mingshuo Zhang, Dan Kong

“…By translating our finding to cohorts of patients with HCC, we demonstrate the specificity of IFN-signaling in the prognosis of patients with HCC and its ability to predict immunotherapy response.Conclusions This study provides a unique single-cell resource with clonal and longitudinal resolution during ICI therapy and reveals IFN signaling as a biomarker of immunotherapy response in HCC, suggesting a beneficial effect by combining IFN inducers with ICIs for patients with HCC.…”
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Full-length transcriptome atlas of gallbladder cancer reveals trastuzumab resistance conferred by ERBB2 alternative splicing by Ziyi Wang, Li Gao, Ziheng Jia, Liguo Liu, Ao Gu, Zhaonan Liu, Qin Zhu, Yichen Zuo, Mingjie Yang, Shijia Wang, Jiyao Ma, Jingyun Zhang, Shimei Qiu, Zhizhen Li, Jinghan Wang, Dongxi Xiang, Fatao Liu, Rong Shao, Yanjing Li, Maolan Li, Wu Wei, Yingbin Liu

“…Overall, this study provides a gallbladder specific long-read transcriptome profile and discovers a novel mechanism of trastuzumab resistance, thus ultimately devising strategies to improve trastuzumab therapy.…”
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Transcriptome and Metabolome Reveal Ferulic Acid as a Critical Phenylpropanoid for Drought Resistance in <i>Dendrobium sinense</i> by Huiyan You, Ao Yi, Qiongjian Ou, Jia Wang, Jun Niu

“…These results demonstrate the crucial role of FA in drought resistance and provide key insights into drought-related metabolic mechanisms.…”
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Spatial transcriptomics of fetal membrane-Decidual interface reveals unique contributions by cell types in term and preterm births. by Lauren S Richardson, Mary Elise Severino, Rahul Chauhan, Weibin Zhang, Marian Kacerovsky, Suresh K Bhavnani, Ramkumar Menon

“…An in-depth understanding of the involvement of each system and cell layer may help provide targeted and tailored interventions to reduce the risk of PTB.…”
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Interaction of blood-entry components, network pharmacology and transcriptomics to elucidate the mechanism of Wentong plaster in treating primary dysmenorrhea by Zongtong Yang, Ziqi Jiao, Cheng Wang, Xiaojing Li, Mengyu Yuan, Zaiyun Sui, Wenhui Wang, Wenjing Hou

“…Network pharmacology and transcriptomics were used to elucidate the underlying mechanisms. …”
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Unraveling yield heterosis in Chinese cabbage hybrid by comparative transcriptomic analysis and LHCB1 gene function analysis by Ruihua Wang, Min Han, Taili Han, Ligong Xu, Yuanyuan Li

“…Currently, few reports on key genes that promote yield advantage formation in Chinese cabbage hybrids exist.MethodsWe conducted a comparative transcriptomic analysis between a Chinese cabbage hybrid (weichunbaiNo.3) and its parents using RNA sequencing, and the differentially expressed genes between the Chinese cabbage hybrid and its parents were confirmed in the rosette and the mature stages. …”
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Integrated transcriptomics and metabolomics analysis of volatiles and variations in carotenoid biosynthesis during different developmental stages of Camellia huana by Zhiping Chen, Yongxin Zhou, Xia Jiang, He Li, Xiaohui Liu, Lunxiu Deng, Gang Wang

“…A total of 12,089 differential genes were screened by transcriptome analysis. Conclusions The results of this study enriched the transcriptome data and provided new insights into the mechanisms of color and odor formation in the flowers of C. huana.…”
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Multi-cohort analysis identifies a blood-based immune transcriptomic signature for early lung cancer detection by Hong Zheng, Aditya M. Rao, Ananthakrishnan Ganesan, Hyongsok Tom Soh, Bruce AJ Ponder, Robert C. Rintoul, Purvesh Khatri

“…The immune system and cancer are intricately linked, which provides a unique opportunity to monitor changes in the immune system as a biomarker of cancer development. …”
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OncoTrace‐TOO: Interpretable Machine Learning Framework for Cancer Tissue‐of‐Origin Identification Using Transcriptomic Signatures by Yang Hao, Haochun Huang, Daiyun Huang, Jianwen Ruan, Xin Liu, Jianquan Zhang

“…Although machine‐learning methods that integrate transcriptomic approaches have provided valuable insights into tumor origins, they often face challenges in distinguishing biologically similar tumors and typically lack biological interpretability. …”
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Comparative transcriptomic analysis of loquat floral fragrance and hormone synthesis regulation across developmental stages in petals and stamens by Jia-Qi Huang, Jia-Qi Wen, Fan Wu, Peng Zhou, Jing-Jing Zhang, Lin-Xuan Wang, Hong-Liang Li

“…This study enriches the molecular mechanism of the release, synthesis and regulation of loquat floral fragrances and provides a theoretical basis for the co-evolutionary pollination between Chinese honey bees and loquat flowers in early winter.…”
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Programmed cell death signatures-driven microglial transformation in Alzheimer’s disease: single-cell transcriptomics and functional validation by Mi-Mi Li, Ying-Xia Yang, Ya-Li Huang, Shu-Juan Wu, Wan-Li Huang, Li-Chao Ye, Ying-Ying Xu

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Single-cell and spatial transcriptomic analysis reveals tumor cell heterogeneity and underlying molecular program in colorectal cancer by Teng Wang, Zhaoming Chen, Wang Wang, Wang Wang, Heng Wang, Shenglong Li

“…However, this heterogeneity offers opportunities for personalized therapy.MethodsThe consensus non-negative matrix factorization algorithm was employed to analyze single-cell transcriptomic data from CRC, which helped identify malignant cell expression programs (MCEPs). …”
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Upper Airway Epithelial Tissue Transcriptome Analysis Reveals Immune Signatures Associated with COVID-19 Severity in Ghanaians by John Demby Sandi, Joshua I. Levy, Kesego Tapela, Mark Zeller, Joshua Afari Yeboah, Daniel Frimpong Saka, Donald S. Grant, Gordon A. Awandare, Peter K. Quashie, Kristian G. Andersen, Lily Paemka

“…We performed bulk transcriptome sequencing of nasopharyngeal samples from severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)-infected Ghanaians with mild and severe COVID-19, as well as healthy controls to characterize immune signatures at the primary SARS-CoV-2 infection site and identify drivers of disease severity. …”
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The short-term effect of nitrogen and phosphorus fertilizers on cold resistance in Urtica cannabina based on transcriptomics and metabolomics analysis by Siqi Liu, Xiaoxue Zhang, Guorui Zhang, Jinmei Zhao, Xiaoqing Zhang, Xiaoqing Zhang

“…Transcriptomics and metabolomics analysis revealed that applying nitrogen and phosphorus fertilizers tended to involve several critical regulatory pathways in the biosynthesis of secondary metabolites, flavonoid biosynthesis, and phenylpropanoid biosynthesis pathways. …”
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A benchmark of RNA-seq data normalization methods for transcriptome mapping on human genome-scale metabolic networks by Hatice Büşra Lüleci, Dilara Uzuner, Müberra Fatma Cesur, Atılay İlgün, Elif Düz, Ecehan Abdik, Regan Odongo, Tunahan Çakır

“…Abstract Genome-scale metabolic models (GEMs) cover the entire list of metabolic genes in an organism and associated reactions, in a tissue/condition non-specific manner. RNA-seq provides crucial information to make the GEMs condition-specific. …”
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Deciphering the regulatory mechanisms of potato cold-induced sweetening via integrated time-course transcriptome and metabolome analysis by Guangcan Cui, Tingting Zhou, Tingting Zhou, Zhongliang Liu, Ting Wang, Qingguo Wang, Tengfei Liu

“…This study aims to decipher the regulatory mechanisms underlying CIS through integrated time-course transcriptome and metabolome analysis. Freshly harvested potato tubers (Solanum tuberosum L. cv. …”
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