Copper Pyrithione Induces Hepatopancreatic Apoptosis and Metabolic Disruption in <i>Litopenaeus vannamei</i>: Integrated Transcriptomic, Metabolomic, and Histopathological Analysis by Jieyu Guo, Yang Yang, Siying Yu, Cairui Jiang, Xianbin Su, Yongfeng Zou, Hui Guo

“…Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of metabolomics and transcriptome revealed that both DEGs and SDMs were enriched in arachidonic acid metabolism, fatty acid biosynthesis, and glycolysis/gluconeogenesis pathways at 3 h, while at 48 h they were enriched in the starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism, and galactose metabolism pathways. …”
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Comparative transcriptome profiling and co-expression network analysis reveals important genes regulating maize response to Southern corn rust by Jialong Liu, Kailai Wang, Nan Wang, Yuan Zhong, Xiuzhen Zhai, Yinsuo Jia, Zhiying Chu, Qing Miao, Hao Su, Mengyun Kou, Huijun Duan, Xiaocui Yan

“…Phenotypic analysis shows that DTMA-50, R99 and P767 have strong resistance, while DTMA-45, N110 and 15B020F3 are more sensitive. …”
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Metabolome and Transcriptome Analysis Reveals the Regulatory Effect of Magnesium Treatment on EGCG Biosynthesis in Tea Shoots (<i>Camellia sinensis</i>) by Zixuan Feng, Zhuan Li, Rui Yan, Nan Yang, Meichen Liu, Yueting Bai, Yuyuan Mao, Chengzhe Zhou, Yuqiong Guo, Yulin Zeng, Yuhang Ji, Yangshun Lin, Jiayong Chen, Shuilian Gao

“…Herein, we performed a comprehensive analysis of the metabolomics and transcriptomics of the shoots of ‘Huangdan’ at five magnesium concentrations: L1-L5 (0, 0.15, 0.45, 0.6, and 0.9 mmol/L mg²⁺, respectively). …”
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Longitudinal transcriptome analysis reveals distinct gene expression patterns in traditional Chinese medicine syndromes of upper respiratory tract infections by Hao Zou, Hao Zou, Changrui Huang, Changrui Huang, Qinqi Feng, Qinqi Feng, Bang Yu, Bang Yu, Jian Liu, Xinyang Shu, Xiaolu Nie, Hongchun Zhang, Xiaohui Zou

“…WC syndrome is marked by mitochondrial dysfunction, while WH syndrome is characterized by downregulated TGF-β and Wnt/β-catenin pathways.…”
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Expression of ABC transporters negatively correlates with ectoine biosynthesis in Halomonas campaniensis under NaCl and ultraviolet mutagenesis treatments revealed by transcriptomi... by Lijuan Qiao, Guoping Shen, Rui Han, Rong Wang, Xiang Gao, Jiangwa Xing, Yanbing Lin, Derui Zhu

“…In this study, we conducted a combined transcriptome-proteome analysis to unveil additional regulatory genes influencing ectoine biosynthesis, particularly under ultraviolet (UV) and salt conditions. …”
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Metabolome integrated with transcriptome, and genome analysis revealed higher accumulations of phytoalexins enhance resistance against Magnaporthe oryzae in new Zhefang rice variet... by Owais Iqbal, Xingrun Yang, Ruoping Wang, Chun Wang, Dandan Li, Jiancheng Wen, Jiasheng Ding, Sauban Musa Jibril, Chengyun Li, Yi Wang

“…Notably, 55% of these metabolites exhibited similar expression patterns across both lines, while 9 DAMs displayed contrasting patterns at 48 h in response to pathogen infection. …”
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Histological, Transcriptomic, and Functional Analyses Reveal the Role of Gibberellin in Bulbil Development in <i>Lilium lancifolium</i> by Shanshan Du, Mengdi Wang, Jiahui Liang, Wenqiang Pan, Qianzi Sang, Yanfang Ma, Mengzhu Jin, Mingfang Zhang, Xiuhai Zhang, Yunpeng Du

“…Silencing these genes resulted in phenotypes similar to <i>LlGA20ox2</i>, inhibiting bulblet development. Further transcriptomic analysis revealed that gibberellin-responsive genes were enriched in the glucuronate pathway, pentose phosphate pathway and galactose metabolism pathways. …”
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A Mouse Model of Polycystic Ovary Syndrome Established Through Subcutaneous Administration of Letrozole Sustained-Release Pellets and Hepatic Transcriptome Analysis by XU Qiuyu, YAN Guofeng, FU Li, FAN Wenhua, ZHOU Jing, ZHU Lian, QIU Shuwen, ZHANG Jie, WU Ling

“…The extent of macrophage infiltration in the liver was evaluated via F4/80 immunohistochemical staining, and hepatic fibrosis levels were observed by Masson's trichrome staining. Transcriptomic sequencing was performed to analyze differentially expressed genes (DEGs) in liver tissues between the control and model groups, followed by enrichment analysis of significant DEGs. …”
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Metabolic, transcriptomic, and proteomic adaptations in pancreatic ductal adenocarcinoma-patient derived xenograft models across serial passages by Pengfei Guo, Haizong Fang, Han Shi, Junrong Zhang, Ge Song, Chongjiu Fan, Xinyu Qiu, Xianchao Lin, Shi Wen, Jianghua Feng, Heguang Huang, Tianhong Teng

“…Transcriptomic and proteomic analyses were performed using RNA-seq and 4D-DIA mass spectrometry, identifying differentially expressed genes (DEGs) and proteins, which were then subjected to enrichment analysis to uncover key biological functions. …”
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Transcriptomic Profiling of Buds Unveils Insights into Floral Initiation in Tea-Oil Tree (<i>Camellia oleifera</i> ‘changlin53’) by Hongyan Guo, Zongshun Zhou, Jian Zhou, Chao Yan, Wenbin Zhong, Chang Li, Ying Jiang, Yaqi Yuan, Linqing Cao, Wenting Pan, Jinfeng Wang, Jia Wang, Tieding He, Yikai Hua, Yisi Liu, Lixian Cao, Chuansong Chen

“…UPLC-MS/MS was used to analyze endogenous gibberellin (GA) concentrations, while transcriptomic analysis was performed to reveal the underlying transcriptional regulatory network. …”
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Comparative gene expression analysis of Beauveria bassiana against Spodoptera frugiperda by Hamdy H. Aly, Yun Meng, Dun Wang

“…Methods A combination of bioassays and transcriptome analysis was employed. S. frugiperda larvae were exposed to different spore concentrations, and mortality rates were recorded at various developmental stages. …”
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Integrative RNA-seq and ATAC-seq analysis unveils antioxidant defense mechanisms in salt-tolerant rice variety Pokkali by Qiaoyu Yang, Yutong Zheng, Xitao Li

“…Abstract Background Salt stress is one of the most significant environmental challenges, severely impacting rice growth and yield. While different rice varieties exhibit varying levels of tolerance to salinity, Pokkali, a traditional salt-tolerant variety, stands out for its ability to thrive in saline conditions. …”
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Genome-wide identification and functional analysis of PEL gene family in Brassica napus L by Man Xing, Yu Kang, Mengjie Lv, Bheem Raj Serani, Qi Shen, Wenfang Jiao, Wen Mu, Shan Chen, Zechuan Peng, Luyao Huang

“…CRISPR/Cas9-mediated knockout of BnaPEL1 increased chlorophyll content, enhanced photosynthesis, and improved yield. Transcriptome analysis revealed that differential genes are involved in carbohydrate metabolism and translation, with key roles in nucleocytoplasmic transport and chlorophyll biosynthesis. …”
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Integrated Volatile Compounds and Transcriptional Gene Analysis Elucidate the Deterioration Mechanism of Embryo Rice During Storage by Xiyuan Yang, Tingting Su, Lixue Ma, Xindi Mu, Hui Wang, Lei Xu, Lidong Wang, Baijun Wang, Di Yao, Changyuan Wang

“…At the same time, volatile compound analysis and transcriptomic analysis were integrated to explore the quality deterioration mechanism of embryo rice during storage. …”
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The Effects of FR and UVA Irradiation Timing on Multi-Omics of Purple Lettuce in Plant Factories by Yubin Zhang, Zhaoxin Li, Ning Zhang, Xiujuan Chai

“…At the transcriptional level, the most extensive transcriptional regulation was observed when FR was applied throughout the entire growth period, and UVA was applied eight days before harvest, significantly impacting pathways such as MAPK signaling cascades, plant hormone signal transduction, photosynthetic processes, and the biosynthesis of secondary metabolites. Metabolomic analysis corroborated the transcriptomic findings, with particular emphasis on antioxidant activity, photoprotection, and defense mechanisms. …”
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An exploratory study of high-throughput transcriptomic analysis reveals novel mRNA biomarkers for acute myocardial infarction using integrated methods by Fei Huang, Zongning Chen, Binjie Tan, Rong He, Xiaoyu Zhang, Yali Chen, Jinsong Gao, Bo Sun

“…This study aims to identify potential mRNA biomarkers in peripheral blood that could aid in the diagnosis and monitoring of AMI. We performed transcriptomic analysis of blood samples from 81 individuals, including 16 healthy controls, 58 AMI patients, and 7 post-treated AMI individuals. …”
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Comparative transcriptome analysis reveals abscisic acid-induced bHLH transcription factors involved in saikosaponin biosynthesis in Bupleurum chinense DC by Han Wang, Shanqun Hu, Tong Li, Xuejie Qu, Jiaqi Zhang, Baoshun Wang, Yixuan Sun, Rui Cao, Yutong Yan, Ze Song, Xia’nan Zhang, Rong Luo, Yuru Tong, Changli Liu

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Stage-specific transcriptomic analysis reveals insights into the development, reproduction and biological function of allergens in the European house dust mite Dermatophagoides pte... by José Cristian Vidal-Quist, Félix Ortego, Bart N. Lambrecht, Stephane Rombauts, Pedro Hernández-Crespo

“…Results Analysis of differentially expressed genes (DEG) revealed that female-biased expression was the most prevalent profile (16% of genes), while males exhibited the highest fold-change differences. …”
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Integration of Transcriptomic Analysis, Network Pharmacology, and Experimental Validation Demonstrates Enhanced Muscle-Protective Effects of Ethanol Extract of Jakyak-Gamcho-Tang by Aeyung Kim, Minh Nhat Tran, A Yeong Lee, Heerim Yeo, Su-Jin Baek, No Soo Kim, Seongwon Cha, Sang-Min Park

“…This comprehensive investigation enabled a detailed assessment of the biological activities of both JGT-E and JGT-W. Transcriptomic analysis revealed that JGT-E significantly modulates key pathways involved in oxidative phosphorylation, mitochondrial biogenesis, and signaling cascades related to PGC-1α, mTORC1, and ERRα, while simultaneously inhibiting TGF-β-mediated muscle atrophic signaling. …”
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Transcriptome Analysis Reveals the Molecular Mechanisms for Mycorrhiza-Enhanced Drought Tolerance in Maize by Regulating the Ca²⁺ Signaling Pathway by Qiaoming Zhang, Wenjing Yang, Miaomiao Wang, Junwei Chen, Zhaoran Zhang, Yanan Wei, Qingshan Chang, Minggui Gong

“…However, comprehensive transcriptome analysis to reveal the molecular mechanism of drought tolerance in the symbiotic process between AMF and maize is still limited. …”
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