Evaluation of <i>Sapindus mukorossi</i> Gaertn Flower Water Extract on In Vitro Anti-Acne Activity by Zibing Zhao, Aohuan Zhang, Liya Song, Congfen He, Huaming He

“…Furthermore, SMFW significantly inhibited the secretion of pro-inflammatory cytokines (TNF-α, IL-6, and IL-β) in lipopolysaccharide (LPS)-stimulated THP-1 macrophages. Transcriptome analysis showed that SMFW treatment reversed 448 LPS-upregulated DEGs and 349 LPS-downregulated DEGs, and KEGG enrichment analysis indicated that SMFW might exert its anti-inflammatory effect via NOD-like receptor and JAK-STAT signaling pathways. …”
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Effects of salicylic acid on the quality of fresh-cut Chinese water chestnuts by Liu Yu, Keyan Lu, Yang Yi, Limei Wang, Wenfu Hou, Youwei Ai, Hongxun Wang, Ting Min

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Enhancement of body red coloration in juvenile spotted scat (Scatophagus argus) by dietary supplementation with Lianjiang red orange peels as a natural carotenoid source by Tong Han, Yongguan Liao, Lei Yang, Xinyi Li, Gang Shi, Dong-Neng Jiang, Chunhua Zhu, Chunhua Zhu, Guangli Li, Hongjuan Shi

“…Additionally, the total carotenoids content in red skin of the G9 group and caudal fin of the G12 group was substantially higher than in the other groups (P &lt; 0.05). By comparative transcriptome analysis of the red skin in G0 and G9 groups, 419 differentially expressed genes (DEGs) were identified, of which 237 were upregulated and 182 were downregulated. …”
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Transcriptomic and Metabolomic Joint Analysis Revealing Different Metabolic Pathways and Genes Dynamically Regulating Bitter Gourd (<i>Momordica charantia</i> L.) Fruit Growth and... by Boyin Qiu, Dazhong Li, Qianrong Zhang, Hui Lin, Yongping Li, Qingfang Wen, Haisheng Zhu

“…In this study, phenotypic observations, metabolomic and transcriptomic analyses, and differential gene expression patterns, along with a correlation analysis, were conducted in different stages of fruit growth and development. …”
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Transcriptome-wide analysis reveals potential roles of CFD and ANGPTL4 in fibroblasts regulating B cell lineage for extracellular matrix-driven clustering and novel avenues for imm... by Hongwei Wang, Yu-nan Zhu, Sifan Zhang, Kexin Liu, Rong Huang, Zhigao Li, Lan Mei, Yingpu Li

“…Weighted Gene Co-expression Network Analysis (WGCNA) was used to identify core genes related to ECM clusters. …”
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Comparative transcriptome-based identification and expression analysis of ATP-binding cassette (ABC) transporters reveals a likely role in the transport of β-caryophyllene and resp... by Haibin Wang, Chen Zong, Yibo Bai, Shuilin Yuan, Yan Li, Tiantian Han, Huanhuan Xu, Chunmei Hu, Xilin Hou, Ying Li

“…Herein, we present a genome-wide comparative transcriptome analysis between non-β-caryophyllene cultivars ('SZQ') and high β-caryophyllene cultivars ('XQC') to identify potential ABC functional gene activities that occur during plant development. …”
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Neoantigen-specific stimulation of tumor-infiltrating lymphocytes enables effective TCR isolation and expansion while preserving stem-like memory phenotypes by Yong Li, Steven A Rosenberg, Paul F Robbins, Zhiya Yu, Maria Parkhurst, Billel Gasmi, Nikolaos Zacharakis, Todd D Prickett, Jared J Gartner, Sri Krishna, Stephanie L Goff, Satyajit Ray, Frank J Lowery, Sivasish Sindiri, Alakesh Bera, Noam Levin, Sanghyun P Kim, Charles A Marquardt, Nolan R Vale, Lior Levy, Tiffany Benzine, Robert V Masi, Rafiqul Islam

“…Single-cell transcriptome analysis revealed that neoantigenic stimulation increased neoantigen-reactive TILs with stem-like memory phenotypes expressing IL-7R, CD62L, and KLF2. …”
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Comparative physiological and co-expression network analysis reveals potential hub genes and adaptive mechanisms responsive to NaCl stress in peanut (Arachis hypogaea L.) by Nan Zhang, Baiyi Bai, Shiyu Zuo, He Zhang, Jingyao Ren, Zhenghao Lv, Dongying Zhou, Haiqiu Yu

“…Transcriptome analysis revealed the presence of 12,612 differentially expressed genes (DEGs) in response to salt stress, with FH23 exhibiting a greater number than NH5. …”
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Integration of bioaccumulations, chemical forms and gene expression responses to understand the transformation and detoxification of inorganic arsenic, cadmium and lead in the brow... by Yanfang Zhao, Yingying Guo, Jifa Wu, Xuming Kang, Xiaofeng Sheng, Zhijun Tan

“…Chemical speciation analysis indicated that S. fusiforme primarily detoxified Cd through organic ligand binding, while Pb was predominantly immobilized as insoluble compounds. …”
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Identification and comparative analysis of genes in response to cold stress between two mainly cultivated tetraploid cottons by QI Bowen, GUO Menglan, LU Hejun, MEI Huan, ZHAO Ting, FANG Lei

“…The results showed that Hai7124 was more sensitive to cold stress than TM-1, and its phenotype changed faster and more obviously under cold stress. Transcriptome analysis showed that TM-1 and Hai7124 contained 8 713 and 12 461 genes in response to cold stress, respectively. …”
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Decoding epithelial–fibroblast interactions in lung adenocarcinoma through single-cell and spatial transcriptomics by Jiajin Yang, Qiuping Xu, Yanjun Lu

“…Cell-cell communication was inferred via CellChat, while metabolic interactions were assessed using MEBOCOST. …”
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Liver transcriptome response to avian pathogenic Escherichia coli infection in broilers with corticosterone treatment by Mengru Chen, Yifei He, Yimin Jia, Lei Wu, Ruqian Zhao

“…Liver transcriptomic analysis identified 768, 335, and 567 differentially expressed genes (DEGs) following CORT, APEC, or both treatments, respectively, enriched in cytokine-cytokine receptor interaction, PPAR signaling pathway, Toll-like receptor signaling pathway, MAPK signaling pathway, steroid hormone biosynthesis pathway, arachidonic acid metabolism, and phagosome pathway, etc., indicating that CORT treatment regulates lipid metabolism and immunity, while APEC infection induces inflammation and disrupts lipid metabolism. …”
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Dissecting crosstalk induced by cell-cell communication using single-cell transcriptomic data by Jiawen Hou, Wei Zhao, Qing Nie

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Transcriptomics profiling of Parkinson’s disease progression subtypes reveals distinctive patterns of gene expression by Carlo Fabrizio, Andrea Termine, Carlo Caltagirone

“…Background Parkinson’s Disease (PD) varies widely among individuals, and Artificial Intelligence (AI) has recently helped to identify three disease progression subtypes. While their clinical features are already known, their gene expression profiles remain unexplored. …”
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Integrating single-cell with transcriptome-proteome Mendelian randomization reveals colorectal cancer targets by Song Wang, Xin Yao, Shenshen Li, Shanshan Wang, Xuyu Huang, Jing Zhou, Xiao Li, Jieying Wen, Weixuan Lan, Yunsi Huang, Hao Li, Yunlong Sun, Xiaoqian Zhao, Qiaoling Chen, Xuedong Han, Ziming Zhu, Xinyue Zhang, Tao Zhang

“…Conclusion By integrating single-cell data, transcriptomic data, proteomic data and GWAS data for MR analysis, we identified CTSF, PCSK7, LYZ, LMAN2L as potential targets for colorectal cancer.…”
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Microbiota transplantation for cotton leaf curl disease suppression—core microbiome and transcriptome dynamics by Ayesha Badar, Rhea Aqueel, Ali Nawaz, Umer Zeeshan Ijaz, Kauser Abdulla Malik

“…Functional pathway analysis reveals upregulation of stress response and metabolism in tolerant species. …”
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Transcriptome analysis of H2O2-treated wheat seedlings reveals a H2O2-responsive fatty acid desaturase gene participating in powdery mildew resistance. by Aili Li, Rongzhi Zhang, Lei Pan, Lichuan Tang, Guangyao Zhao, Mingzhu Zhu, Jinfang Chu, Xiaohong Sun, Bo Wei, Xiangqi Zhang, Jizeng Jia, Long Mao

“…However, the effect of H(2)O(2) stress on the bread wheat transcriptome is still lacking. To investigate the cellular and metabolic responses triggered by H(2)O(2), we performed an mRNA tag analysis of wheat seedlings under 10 mM H(2)O(2) treatment for 6 hour in one powdery mildew (PM) resistant (PmA) and two susceptible (Cha and Han) lines. …”
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Integrated transcriptomics and metabolomics to explore the mechanisms of Elaeagnus mollis diels seed viability decline by Ren Ruifen, Guo Jiayi, Ji Zhe, Du Shuhui, Yang Xiuyun

“…Transcriptomic results showed that a total of 801 differentially expressed genes (DEGs) were identified between fresh and 1-month-stored seeds, while 1,524 were identified between fresh and 3-month-stored seeds. …”
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Insight into the composition and differentiation of endophytic microbial communities in kernels via 368 maize transcriptomes by Fang Tao, Feng Chen, Haida Liu, Cheng Chen, Beijiu Cheng, Guomin Han

“…Beneficial bacteria were predominant in the core species of networks in TST kernels, while pathogenic bacteria were more abundant in the core species of networks in NSS kernels. …”
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Genetic background and oncogenic driver determines the genomic evolution and transcriptomics of mammary tumor metastasis by Christina R. Ross, Karol Szczepanek, Jack Sanford, Gabriel Needle, Tinghu Qiu, Larry Pearce, Maxwell P. Lee, Kent W. Hunter

“…Transcriptome analysis demonstrated that oncogenic drivers strongly shaped metastasis-specific gene expression (MSGE), with each driver exhibiting distinct expression profiles. …”
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