Transcriptome-Wide Analysis of N6-Methyladenosine-Modified Long Noncoding RNAs in Particulate Matter-Induced Lung Injury by Yingying Zeng, Guiping Zhu, Wenjun Peng, Hui Cai, Chong Lu, Ling Ye, Meiling Jin, Jian Wang

“…Conclusions: This study first provides a comprehensive transcriptome-wide analysis of m⁶A methylation profiling in lncRNAs associated with PM-induced lung injury and identifies three pivotal candidate m⁶A-modified lncRNAs. …”
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Transcriptomic profiling identifies ferroptosis and NF-κB signaling involved in α-dimorphecolic acid regulation of microglial inflammation by Xiao-Xi Zhu, Pei-Juan Wang, Shan Chao, Wei-Jia Tang, Long-You Zhao, Li-Mei Yu, Fan Yang

“…Conclusion α-DIPA inhibits microglial inflammation likely through regulating the pathways of the ferroptosis and NF-κB signaling. These results provided preliminary evidence for α-DIPA as a potential therapeutic candidate for neurodegenerative diseases like MS.…”
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Genome-wide association study and transcriptome analysis reveal candidate genes related to drought stress in the germination stage of soybean by Keke Kong, Mengge Xu, Lanhua Wu, Huiwen Zhou, Ruikai Wang, Tuanjie Zhao, Chune Wang, Yingpei Song

“…In addition, by combining RTM-GWAS and transcriptome analysis, 22 candidate genes underlying large-contribution QTLs were identified. …”
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Transcriptome and targeted metabolome analysis of lipid profiles, nutrients compositions and volatile compounds in longissimus dorsi of different pig breeds by Zhen Luo, Ting Lai, Yijia Fan, Chengbin Yu, Wei Li, Meng Li, Shenghui Lei, Jing Zhang, Weina Xu, Zhe Wang, Jianxiong Xu

“…Conclusion Our study provided new insights into potential mechanisms of IMF deposition, nutrients composition and volatile compounds of muscular tissues of different pig breeds.…”
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Effects of acute cadmium exposure on biochemistry, liver oxidative stress and transcriptomics in Songpu mirror carp (Cyprinus carpio Songpu) by Ze Fan, Yan Wang, Chenhui Li, Di Wu, Liansheng Wang, Jinnan Li, Jiaxin Li, Linghong Miao, Hong Xu

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Integrative transcriptomic-physiological analysis deciphers nitrogen-mediated carbon reallocation balancing growth and flavonoid metabolism in Epimedium pubescens by Shangnian Liu, Shangnian Liu, Xiaojing An, Xiaojing An, Chaoqun Xu, Dongmei He, Xianen Li, Caixia Chen, Baolin Guo, De Xu, Juan Huang

“…A tripartite regulatory network linking nitrogen-responsive genes (e.g., EpF3H, UGT), Icariin-type flavonoid/carbon metabolism (e.g., icariin, soluble sugars), and growth phenotypes (e.g., biomass, photosynthesis) elucidated how nitrogen optimizes the trade-off between medicinal quality and yield in E. pubescens. This study provides molecular targets for precision nitrogen management to enhance both medicinal quality and yield, while establishing an integrative framework combining physiological and transcriptomic analyses to investigate metabolic trade-offs in non-model plants.…”
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Revealing the Mechanism of <i>Hemerocallis citrina</i> Baroni in Depression Treatment Through Integrated Network Pharmacology and Transcriptomic Analysis by Shan Gao, Jihui Lu, Yixiao Gu, Yaozhi Zhang, Cheng Wang, Feng Gao, Ziqi Dai, Shujing Xu, Jindong Zhang, Yuqin Yang, Haimin Lei

“…Results from network pharmacology and transcriptomics indicated that the PI3K/Akt/CREB signaling pathway is essential for the therapeutic effects of HCB on depression. …”
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Integrative single-cell and cell-free plasma RNA transcriptomics identifies biomarkers for early non-invasive AD screening by Li Wu, Li Wu, Renxin Zhang, Renxin Zhang, Yichao Wang, Yichao Wang, Shaoxing Dai, Shaoxing Dai, Naixue Yang, Naixue Yang

“…The 34-gene panel provides non-invasive molecular insights into AD pathogenesis and early screening. …”
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Comparative transcriptome analysis of differentially expressed genes of Medicago falcata L. breeding lines response to saline-alkaline stress by Hua Chai, Xiaolong Wang, Zhao Yang, Shasha Li, Yanxia Xu, Yue Wu, ZhongBao Shen

“…Furthermore, physiological indicators such as chlorophyll content, proline accumulation, and superoxide dismutase (SOD) activity were assessed to compare the responses of LM18 and HL to salt-alkali stress. By integrating transcriptomic and physiological analyses, this study provides new insights into the physiological and molecular regulatory mechanisms of M. falcata in response to salt-alkali stress. …”
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Cryptosporidium parvum infection alters the intestinal mucosa transcriptome in neonatal calves: impacts on epithelial barriers and transcellular transport systems by Arash Veshkini, Christa Kühn, Christa Kühn, Franziska Dengler, Lisa Bachmann, Lisa Bachmann, Wendy Liermann, Christiane Helm, Reiner Ulrich, Cora Delling, Harald M. Hammon

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Integrated morphophysiological, transcriptomic, and metabolomic data uncover the molecular mechanism of environmental adaptation of Zanthoxylum armatum with different latitudinal g... by Yuan Guo, Xueqian Fu, Chong Sun, Chong Sun, Yifei Deng, Han Liu, Long Tong, Mi Kuang, Ning Tang, Wenying Yang, Xia Liu, Zexiong Chen

“…Morphological, physiological, and biochemical traits were measured, including stomatal density, nutrient content, antioxidant capacity, and chlorophyll level. Transcriptomic and metabolomic profiling were conducted using RNA-seq and UPLC-MS/MS, respectively. …”
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Integrative analyses of morpho-physiological, biochemical, and transcriptomic reveal the seedling growth response of Pinus yunnanensis to nitrogen and phosphorus fertilization by Junfei Xu, Junfei Xu, Xiyan Li, Shi Chen, Shi Chen, Lin Chen, Lin Chen, Junrong Tang, Junrong Tang, Peizhen Chen, Peizhen Chen, Nianhui Cai, Nianhui Cai, Yulan Xu, Yulan Xu

“…In conclusion, this study provides comprehensive information on the response of seedlings to varying proportions of N and P and may promote the growth of P. yunnanensis seedlings by optimizing the proportion of N and P in fertilizers.…”
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A single-cell transcriptomic atlas of human lens epithelium: identification and functional insights into lens stem/progenitor cells by Yuzhou Gu, Lu Chen, Shuying Chen, Yuhao Wu, Shengjie Hao, Feiyin Sheng, Jiali Yuan, Zhenwei Qin, Di Wu, Yu Han, Zengying Yao, Zhijian Chen, I. Michael Wormstone, Yibo Yu, Junbin Qian, Qiuli Fu, Ke Yao

“…CytoTRACE analysis to the LEC and LFC data sets provided a differentiation trajectory. The TAC group was determined as stage 2 in the trajectory and LFCs last. …”
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Integrated single-cell and transcriptomic analysis of bone marrow-derived metastatic neuroblastoma reveals molecular mechanisms of metabolic reprogramming by Jing Chu, Rong Qin, Shu-Jing Wang, Qiang Wang, Qiang Wu

“…These findings suggest that integrated strategies targeting both tumor metabolism and the immune microenvironment may provide new avenues for the treatment of high-risk, metastatic NB.…”
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Temporal transcriptomic changes in the THY-Tau22 mouse model of tauopathy display cell type- and sex-specific differences by Muhammad Ali, Pierre Garcia, Laetitia P. Lunkes, Alessia Sciortino, Melanie H. Thomas, Tony Heurtaux, Kamil Grzyb, Rashi Halder, Alexander Skupin, Luc Buée, David Blum, Manuel Buttini, Enrico Glaab

“…Conclusions This study provides a comprehensive single-cell transcriptomic characterization of sex-linked and age-dependent changes in the THY-Tau22 tauopathy model, revealing new insights into the interplay between age-dependent AD-like pathologies and sex. …”
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snRNA‐Seq and Spatial Transcriptome Reveal Cell–Cell Crosstalk Mediated Metabolic Regulation in Porcine Skeletal Muscle by Liu Guo, Mengmeng Han, Junfei Xu, Wenyue Zhou, Hanjing Shi, Sisi Chen, Weijun Pang, Xing Zhang, Yehui Duan, Yulong Yin, Fengna Li

“…Both snRNA‐seq and spatial transcriptome pointed out that FAPs are the important source of secretory proteins. …”
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Unveiling migraine subtype heterogeneity and risk loci: integrated genome-wide association study and single-cell transcriptomics discovery by Shuxu Wei, Yan Quan, Xinyi Li, Suiqin Zhong, Ling Xiao, Chao Yang, Ronghuai Shen, Xiaojia Lu, Lingbin He, Youti Zhang, Xianxi Huang

“…Methods We integrated genome-wide association study (GWAS) data from FinnGen R11 and international cohorts with transcriptomic, epigenomic, and spatially resolved single-cell spatial transcriptomics (sc-ST) profiles. …”
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Identification of Gene Pathways Involved in Tolerance to End-of-Season Drought Stress in the Dayton/Ranney Barley Genotype using Transcriptomics by Saeedeh Alidoust, Sara Dezhsetan, Mahdi Behnamian

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Single-cell RNA sequencing provides new insights into the interaction between astrocytes and neurons after spinal cord injury in mice by Zhi Tang, Hengyang Lu, Xiao Yang, Mao Wu, Junfeng Yang, Shaoshuo Li, Heng Liu, Junkang Zhou, Bin Tang, Xinyao Du, Fei Xu, Yang Shao, Jianwei Wang

“…Methods and results: In this study, single-cell RNA sequencing (scRNA-seq) was used to analyze the transcriptome data of acute, subacute and intermediate stages of SCI in mice as well as normal tissues. …”
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Alanine Derived from Ruminococcus_E bovis Alleviates Energy Metabolic Disorders during the Peripartum Period by Providing Glucogenic Precursors by Fanlin Kong, Shuo Wang, Yijia Zhang, Chen Li, Dongwen Dai, Yajing Wang, Zhijun Cao, Hongjian Yang, Shengli Li, Wei Wang

“…By using ketosis peripartum dairy cows as a model, this study aims to elucidate the metabolic mechanism of peripartum cows and provide a novel way for managing energy metabolic disorders. …”
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