Multi-region brain transcriptomic analysis of amyotrophic lateral sclerosis reveals widespread RNA alterations and substantial cerebellum involvement by Natalie Grima, Andrew N. Smith, Claire E. Shepherd, Lyndal Henden, Thiri Zaw, Luke Carroll, Dominic B. Rowe, Matthew C. Kiernan, Ian P. Blair, Kelly L. Williams

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Combined transcriptome and metabolome analysis provides insight into the ERF073 – Malic acid network in pakchoi under submergence stress by Dan-dan Xi, Lu Gao, Li-ao Ge, Hong-fang Zhu, Li-ming Miao, Ding-yu Zhang, Chang-wei Zhang, Ying Li, Yan-xiao Dong, Xi-lin Hou, Yu-ying Zhu, Zhao-hui Zhang, Xiao-feng Li

“…Leaves from 1 h stress, 5 h stress, and subsequent 5-h recovery phases were harvested for metabolome and transcriptome analyses. Data analysis revealed that 206 differentially accumulated metabolites (DAMs) were identified between SZQ and HYD after 1 h stress (S1 vs H1) and 330 DAMs were identified between SZQ and HYD after 5 h stress (S5 vs H5) at stress stage. …”
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Transcriptome Analysis of <i>Sclerotium rolfsii</i>: Unraveling Impact of Glycolytic Pathway on Substrate Utilization and Microbial Polysaccharide Production by Jia Song, Junfeng Li, Chenrui Zhen, Juan Du, Rui Zhao, Bingqian Fan, Jiayi Hou, Bingning Gao, Yu Zheng, Linna Tu, Min Wang

“…In this study, we performed a transcriptomic analysis on the mycelium of <i>S. rolfsii</i> fermented with different carbon sources. …”
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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

“…Finally, in vitro experiments were carried out to validate the roles of selected genes in regulating NB cell proliferation, migration, invasion, and mitochondrial function. Single-cell transcriptomic analysis of bone marrow–derived NB samples identified nine distinct cell subpopulations with diverse intercellular communication networks. …”
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Integrative physiological and transcriptomic analysis provides insights on the molecular basis of ABA-enhanced drought tolerance in pear (Pyrus betulaefolia) by Guo-Ling Guo, An-Ran Luo, Yun-Hui Tan, Rui-Kang Yuan, Ting-Yue Luo, Pan-Pan Ma, Jun-Yu Zhan, Piao Han, Li Liu, Wei Heng, Zhenfeng Ye, Sheng Yang, Bing Jia

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Transcriptome analysis indicates improved adipose tissue function in growing Iberian pig fed olive by-products based diets by Patricia Palma-Granados, Patricia Palma-Granados, Juan M. García-Casco, Juan M. García-Casco, Ramón Peiró-Pastor, Cristina Óvilo, Miguel A. Delgado, Miguel A. Delgado, Fabián García, Adrián López-García, Adrián López-García, Elena González, María Muñoz

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Transcriptome analysis revealed that AcWRKY75 transcription factor reduced the resistance of kiwifruit to Pseudomonas syringae pv. actinidiae by Lixia Ye, Minmin Luo, Yafang Wang, Yafang Wang, Mengqi Yu, Mengqi Yu, Zhi Wang, Fuxi Bai, Xuan Luo, Li Li, Qiong Huang, Jue Peng, Qi Chen, Qinghong Chen, Lei Gao, Lei Zhang

“…In this study, we evaluated the Psa resistance of six hybrid populations and screened a resistant segregation population R1F2. Then, transcriptome analysis on the Psa extremely high-resistant (HR) and extremely high-susceptible (HS) plants of the R1F2 population was performed. …”
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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

“…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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Study on molecular mechanism of intervertebral disc degeneration by single cell hdWGCNA combined with transcriptome sequencing by Xuan Zhao, Qijun Wang, Wei Wang, Xiaolong Chen, Shibao Lu

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Semen Quality, Testicular Cell Apoptosis, and Transcriptome Analysis Following Mild Scrotal Heat Stress in Wugu–Hu Crossbred and Hu Rams by Shikun Chen, Mingxu Jiang, Yanyun Wang, Qingjie Pan, Henry Annandale, Peter Charles Irons, Huansheng Dong

“…Wugu–Hu rams demonstrate more transcriptomic changes. Further GO analysis revealed enrichment in spermatogenesis-related processes, while KEGG analysis identified Oocyte meiosis and cell cycle pathways, with a downregulation of key genes (CDK1, CDK2, CDC20, and PLK1) indicating impaired meiosis in Wugu–Hu rams. …”
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Physiological and Transcriptome Analysis Reveal the Underlying Mechanism of Salicylic Acid-Alleviated Drought Stress in Kenaf (<i>Hibiscus cannabinus</i> L.) by Hui Zhang, Guofeng Xu, Samavia Mubeen, Rujian Wei, Muzammal Rehman, Shan Cao, Caijin Wang, Jiao Yue, Jiao Pan, Gang Jin, Ru Li, Tao Chen, Peng Chen

“…In this study, the kenaf seedlings were subjected to physiological and transcriptomic analysis under control (CK), moderate drought stress (D), and moderate drought stress with 1 mM SA (D_SA). …”
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The Hedyotis diffusa chromosome-level genome and multi-omics analysis provide new insights into the iridoids biosynthetic pathway by Pengyu Chen, Pengyu Chen, Zhuang Huang, Zhuang Huang, Mingzhu Yin, Yu-xin Wen, Yu-xin Wen, Qi Jiang, Qi Jiang, Ping Huang, Rui Qian, Rui Qian, Xing Hong, Xing Hong, Kaojiang Zhu, Kaojiang Zhu, Benjiang Xiao, Benjiang Xiao, Meng Chen, Meng Chen, Shihao Li, Shihao Li, Fang Huang, Lin-tao Han, Lin-tao Han

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Integrative analysis of semaphorins family genes in colorectal cancer: implications for prognosis and immunotherapy by Jiahao Zhu, Benjie Xu, Zhixing Wu, Zhixing Wu, Zhiwei Yu, Shengjun Ji, Jie Lian, Haibo Lu

“…However, the prognostic value of SEMA-related genes in colorectal cancer (CRC) remains unclear.MethodsWe applied a novel machine learning framework that incorporated 10 machine learning algorithms and their 101 combinations to construct a SEMAs-related score (SRS). Multi-omics analysis was performed, including single-cell RNA sequencing (scRNA-seq), and spatial transcriptome (ST) to gain a more comprehensive understanding of the SRS. …”
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Unveiling Salt Tolerance Mechanisms and Hub Genes in Alfalfa (<i>Medicago sativa</i> L.) Through Transcriptomic and WGCNA Analysis by Fengdan Wang, Hanfu Wu, Mei Yang, Wen Xu, Wenjie Zhao, Rui Qiu, Ning Kang, Guowen Cui

“…In the above, comparisons between varieties were conducted based on the relative values of the indicators in relation to their controls. Transcriptomic analysis revealed that under salt stress, Longmu801 had 16,485 differentially expressed genes (DEGs) relative to its control, while WL168 had 18,726 DEGs compared to its control. …”
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Selenium Alleviates Cadmium Toxicity by Regulating Carbon Metabolism, AsA-GSH Cycle, and Cadmium Transport in <i>Glycyrrhiza uralensis</i> Fisch. Seedlings by Xuerong Zheng, Jiafen Luo, Xin Li, Chaoyue Zhang, Guigui Wan, Caixia Xia, Jiahui Lu

“…Additionally, the treatment reduced the malondialdehyde (MDA) content by 30.71% and 58.91% at 12 h and 30 d, respectively. The transcriptome analysis results suggest that Se mitigated Cd toxicity by enhancing carbon metabolism, regulating the AsA-GSH cycle, reducing Cd absorption, promoting Cd transport and compartmentalization, and modulating Cd resistance-associated transcription factors. …”
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Transcriptome analysis reveals nutrient deprivation reduces nitrate content in lettuce (Lactuca sativa var. ramosa Hort.) and enhances nitrogen metabolism by Yingying Zhang, Xuena Liu, Shikai La, Mingjiao Wang, Xu Hu, Ainong Shi, Jinghua Guo, Lingdi Dong

“…Nitrate transporter genes NRT2.4 and NRT2.5 were upregulated in roots, while NRT1 was induced in leaves, suggesting enhanced nitrate redistribution. …”
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The Impact of Dissolved Biochar on Oxidative Stress and Its Effect on the Virulence of <i>Steinernema feltiae</i>: Implications for Biocontrol Efficiency by Xinrui Wang, Jie Li, Jing Li, Lan Luo, Gang Li, Weibin Ruan, Guilong Zhang

“…As revealed by virulence assays, DBC treatment reduced the infectivity of EPNs against <i>Galleria mellonella</i> larvae. Transcriptome analysis revealed that DBC primarily affected oxidative stress response, membrane transport, and longevity regulation pathways. …”
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Melatonin-induced Bacillus tequilensis enhanced the disease resistance of Camellia oleifera against anthracnose by modulating cell wall and phenylpropanoid metabolism by Aiting Zhou, Aiting Zhou, Huiqin Zhou, Huiqin Zhou, Ruiqi Peng, Ruiqi Peng, Di Liu, Di Liu, Jianrong Wu, Jianrong Wu, Jia Deng, Jia Deng, Fang Wang, Fang Wang

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Exploring potentially synthetic genes related to diarrhetic shellfish toxins production in Prorocentrum sp. via comparative transcriptomics by Danlin Zheng, Jingyi Cen, Peiliang Chen, Ligong Zou, Jian Zou, Qun Li, Songhui Lu

“…We conducted a comprehensive comparative transcriptomic analysis to identify potential toxin-related genes, focusing on polyketide synthases (PKSs) and fatty acid synthases (FASs). …”
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Integrative Analysis of Transcriptomic and Metabolomic Profiles Identifies Distinct Dynamic Changes in Primary and Secondary Metabolites in Grape Berries Under Fruit-Specific Light... by Xuan Luo, Jiahao Wu, Hongjuan Li, Xintong Wang, Wendi Wang, Hui Li, Kunfeng Li, Songling Bai

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