Integrated Analysis of the Transcriptome and Metabolome Reveals the Network Regulating Fruit Taste in Sponge Gourd (<i>Luffa cylindrica</i>) by Yaqian Chai, Wenjing Qiu, Zhikun Li, Luyao Gao, Wenqi Dong, Peng Zhang, Shengjun Zhou, Xin Wang, Yuqiang Zhu, Yuyan Sun

“…Similarly, the lysine, phenylalanine, and tryptophan contents were higher in GT than in BT (1.48-, 1.60-, and 1.38 times higher, respectively). Transcriptomic analysis of GT and BT fruits identified 1821 upregulated and 1185 downregulated differentially expressed genes (DEGs) in GT, while metabolomic analysis detected 25 upregulated differentially accumulated metabolites (DAMs) and 28 downregulated DAMs in GT. …”
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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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Transcriptomic and Metabolomic Analysis Reveal the Effects of Light Quality on the Growth and Lipid Biosynthesis in <i>Chlorella pyrenoidosa</i> by Tingting Zhu, Ge Guan, Lele Huang, Lina Wen, Linxuan Li, Maozhi Ren

“…Transcriptomic and metabolomic analysis indicated that both red and blue light positively regulate lipid synthesis in <i>Chlorella pyrenoidosa</i>, but they exhibited distinct impacts on the fatty acid compositions. …”
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Genetic insights into alcohol-associated liver disease: integrative transcriptome-wide analysis identifies novel susceptibility genes by Qianchang Wang, Zhe Wang, Minzhe Hu, Fangfeng Liu, Fangfeng Liu, Zhengjian Wang

“…BackgroundAlcohol-associated liver disease (ALD) is a chronic condition influenced by both genetic and environmental factors. While GWAS has identified ALD-related loci (PNPLA3, MBOAT7, TM6SF2), underlying genetic mechanisms and therapeutic targets remain unclear.MethodsThis study utilized the FinnGen R12 dataset (488,982 participants) and GTEx v8 eQTL data to perform a cross-tissue transcriptome-wide association study (TWAS) using UTMOST, with single-tissue validation via FUSION. …”
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Transcriptomic and metabolomic analysis reveals hepatic lipid metabolism disruption in Japanese quail under polystyrene microplastics exposure by Xinxin Zhang, Lingyang Jing, Xiaoqing Pei, Qingyu Zhang, Hongfeng Zhao

“…In this study, we attempted to determine the hepatotoxic effects of MPs exposure on birds by using a laboratory model animal-Japanese quail (Coturnix japonica) through integrating transcriptomic and metabolomic analysis. Seven-day old female chicks were exposed to low concentrations (0.02 mg/kg, 0.4 mg/kg) and high concentration (8 mg/kg) polystyrene microplastics (PS-MPs) of environmental relevance in the feed for 35 days. …”
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Unraveling tissue-specific molecular mechanisms orchestrating arsenic response processes in Pteris vittata through transcriptomic analysis by Shujun Wei, Ryota Moriuchi, Christine Dwi A.P. Wiyono, Chihiro Inoue, Mei-Fang Chien

“…Therefore, in this study, we investigated As - related processes by conducting transcriptomic analysis on hydroponically grown P. vittata exposed to 500 ppb arsenate (AsV). …”
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Bioinformatic Analysis of Apoptosis-Related Genes in Preeclampsia Using Public Transcriptomic and Single-Cell RNA Sequencing Datasets by Liu L, Li X, Yang H, Xu F, Dong X

“…Endothelial cell communication with other cell types decreased, while the interaction between common myeloid progenitors (CMP) and villous cytotrophoblasts (VCT) enhanced. …”
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Transcriptomic profiling and machine learning reveal novel RNA signatures for enhanced molecular characterization of Hashimoto’s thyroiditis by Zefeng Li, Qiuyu Xu, Fengxu Xiao, Yipeng Cui, Jue jiang, Qi Zhou, Jiangwei Yan, Yu Sun, Miao Li

“…Abstract While ultrasonography effectively diagnoses Hashimoto’s thyroiditis (HT), exploring its transcriptomic landscape could reveal valuable insights into disease mechanisms. …”
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Combined Analysis of Transcriptome and Mendelian Randomization Reveals AKT1 and PPARG as Biomarkers Related to Glucose Metabolism in Sepsis by Ma J, Li W, Ma Q, Ding L, Wang Z, Wang R, Huang Y, Ma G, Gao J

“…The diagnostic nomogram based on these biomarkers showed good efficacy. Enrichment analysis suggested AKT1 inhibits sepsis development, while PPARG promotes it. …”
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Integrative analysis of metabolomics and transcriptomics reveals alterations in egg quality and hepatic lipid metabolism in hens supplemented with curcumin by Cunzhi Zou, Haiyu Jiang, Xuanfu Wu, Jiang Gao, Wenqiang Ma

“…Transcriptomic analysis revealed that curcumin primarily upregulated key genes involved in hepatic cholesterol synthesis (Fdft1, Sqle, Cyp51A1, Msmo1, and Dhcr24) and downregulated key genes involved in hepatic TG synthesis (Acaca, Acacb, and Fasn). …”
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Integrative Transcriptome and Metabolome Analysis Identifies Potential Pathways Associated with Cadmium Tolerance in Two Maize Inbred Lines by Pingxi Wang, Min Li, Xingye Ma, Bin Zhao, Xining Jin, Huaisheng Zhang, Shilin Chen, Xiangyuan Wu, Xiaoxiang Zhang

“…Transcriptomic analysis identified 3030 differentially expressed genes (DEGs) unique to C7_2 and 4298 DEGs unique to Z58, with 1746 common DEGs shared between the two lines. …”
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Integrated transcriptomic and metabolomic analysis reveals the effects of EMMPRIN on nucleotide metabolism and 1C metabolism in AS mouse BMDMs by Yun Zhang, Diyuan Zhang, Zulong Xie, Tianli Xia, Lili Zou, Tao Wang, Li Zhong, Zhuo Zeng, Lingying Wang, Guozhu Chen, Xing Liang

“…Seahorse assay confirmed reduced glycolysis and oxidative phosphorylation (OXPHOS) levels and the Oil Red O staining confirmed the decrease of lipid droplets in siE group.ConclusionThe integrated metabolomic and transcriptomic analysis suggested that nucleotide metabolism and 1C metabolism may be major metabolic pathways affected by siEMMPRIN in AS mouse BMDMs. …”
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Improving reproducibility of differentially expressed genes in single-cell transcriptomic studies of neurodegenerative diseases through meta-analysis by Nathan Nakatsuka, Drew Adler, Longda Jiang, Austin Hartman, Evan Cheng, Eric Klann, Rahul Satija

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Comparative Transcriptome Analysis of Gene Responses of Salt-Tolerant and Salt-Sensitive Watermelon Cultivars’ Roots to Salt Stress by Peng Liu, Chao Gao, Shuai Li, Xudong Wang, Yumei Dong, Chongqi Wang, Zigao Jiao, Jianlei Sun

“…The provided physiological data demonstrate that T23 exhibits superior antioxidant and osmoregulatory abilities relative to B2. The transcriptome analysis identified differentially expressed genes (DEGs) between the two cultivars under salt stress, with T23 showing the highest number of DEGs at 6 h, while B2 exhibited a significant increase in DEGs at 168 h. …”
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Comparative transcriptome analysis reveals the potential mechanism of seed germination promoted by trametenolic acid in Gastrodia elata Blume by Jie Liu, Wangyang Ye, Danyang Wang, Hongqi Zhang, Junzhi Wang, Dongwei Li

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Gonadal transcriptome analysis reveals MAG participates in ovarian suppression of intersex red claw crayfish (Cherax quadricarinatus) by Honglin Chen, Miaofeng Ouyang, Huan Zhou, Fangfang Liu, Huiyi Cai, Bao Lou

“…Results In this study, the structure and transcriptomic profiles of ovotestis and female and male gonad was analysis and compared, 406 differentially expressed genes were identified, among which membrane-anchored AG-specific factor (MAG) exhibited significantly greater expression in ovotestis gonads than in male or female gonads. …”
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Differential photosynthetic responses to drought stress in peanut varieties: insights from transcriptome profiling and JIP-Test analysis by Jingyao Ren, Pei Guo, Xinhua Zhao, Xinlei Ma, Xin Ai, Jing Wang, Hongtao Zou, Haiqiu Yu

“…To dissect photosynthetic apparatus dynamics, we implemented JIP-test analysis of chlorophyll fluorescence kinetics. Both cultivars exhibited substantial increases in Vj and Vi parameters at 24 h, while FH18 demonstrated a pronounced elevation in Vk during the O-J phase transition, suggesting severe impairment of the oxygen-evolving complex. …”
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A rare IDH-Mutant glioma case: insights from single-cell transcriptomic analysis of tumor recurrences by Wen Li, Yuanshuai Zhou, Shaheryar Shafi, Jun Dong, Minxuan Sun

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Comparative transcriptome analysis reveals key long noncoding RNAs for cadmium tolerance in Tibetan hull-less barley by Md Rafat Al Foysal, Md Rafat Al Foysal, Cheng-Wei Qiu, Feibo Wu

“…Among these, 1884 target genes were regulated by cis-acting lncRNAs, while 3428 were regulated by trans-acting lncRNAs. …”
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Aberrant c-AMP signalling in richter syndrome revealed by single-cell transcriptome and 3D chromatin analysis by Heng Li, Cheng Xing, Ji Li, Yihao Zhan, Ming Luo, Peilong Wang, Yue Sheng, Hongling Peng

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