Decoding the Tumor Microenvironment of Myoepithelial Cells in Triple-Negative Breast Cancer Through Single-Cell and Transcriptomic Sequencing and Establishing a Prognostic Model Ba... by Xiaocheng Yu, Ye Tian, Rui Zhang, Yong Yang

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Integrated Metabolomic and Transcriptomic Analysis Reveals the Molecular Regulatory Mechanism of Gamma-Aminobutyric Acid Accumulation in White Quinoa (<i>Chenopodium quinoa</i> Wil... by Mengying Wu, Qian Zhou, Yasai Sun, Liangfu Zhou, Dongyao Li, Ting Ren, Yu Zheng, Wen Zhao, Jie Wang

“…Through the comprehensive integration of metabolome and transcriptome data, an association was revealed between GABA accumulation, 9 differentially expressed metabolites, and 27 differentially expressed genes. …”
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Integrated analysis of single-cell RNA-seq and spatial transcriptomics to identify the lactylation-related protein TUBB2A as a potential biomarker for glioblastoma in cancer cells... by Yifan Xu, Chonghui Zhang, Jinpeng Wu, Pin Guo, Nan Jiang, Chao Wang, Yugong Feng

“…By reconstructing the spatial transcriptomics of hematoxylin and eosin (HE)-stained sections, we further evaluated the lactylation activity in GBM tissues. …”
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Knowledge of the genetics of human pain gained over the last decade from next-generation sequencing by Dario Kringel, Jörn Lötsch

“…Next-generation sequencing (NGS) technologies have revolutionized pain research by providing comprehensive insights into genetic variation across the genome. …”
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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

“…In summary, these observations open up new future research directions for β-caryophyllene transport and provide insight into ABC family genes in Brassica campestris.…”
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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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Transcriptomic analysis reveals genetic factors underlying impaired symbiotic nitrogen fixation in lines derived from crosses between cultivated peanut (Arachis hypogaea L.) and it... by Darius Tchoutang Nzepang, Maïmouna Cissoko, Djamel Gully, Valérie Hocher, Jean-François Rami, Saliou Fall, Daniel Fonceka, Sergio Svistoonoff

“…Results A comparative analysis of the transcriptome profiles of the CSSLs and Fleur11 revealed significant changes in the expression of genes involved in plant immune signaling and key symbiotic genes, such as NIN, EFD, FEN1 or SNF-related transporters. …”
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Whole-Transcriptome RNA Sequencing Reveals Significant Differentially Expressed mRNAs, miRNAs, and lncRNAs and Related Regulating Biological Pathways in the Peripheral Blood of COV... by Cai-xia Li, Jian Chen, Shu-kai Lv, Jin-hui Li, Lei-lei Li, Xiao Hu

“…In this study, fourteen peripheral blood samples from COVID-19 patients (n=10) and healthy donors (n=4) were collected to perform the whole-transcriptome sequencing. Lung tissues of COVID-19 patients (70%) presenting with ground-glass opacity. …”
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Identification of Isoflavonoid Biosynthesis-Related R2R3-MYB Transcription Factors in Callerya speciosa (Champ. ex Benth.) Schot Using Transcriptome-Based Gene Coexpression Analysi... by Linchan Yu, Ding Huang, Jinyuan Gu, Dongjin Pan, Yong Tan, Rongshao Huang, Shaochang Yao

“…Here, a total of 101 R2R3-MYB TFs were identified from C. speciosa transcriptome dataset. 25 clades divided into five functional groups were clustered based on the sequence similarity and phylogenetic tree. …”
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Identification of Auxin-Associated Genes in Wheat Through Comparative Transcriptome Analysis and Validation of the Candidate Receptor-like Kinase Gene <i>TaPBL7-2B</i> in Arabidops... by Mengjie Zhang, Guangzhu Chen, Jie Cai, Yongjie Ji, Linrun Xiang, Xinhong Chen, Jun Wang

“…In this study, we conducted a comparative transcriptome analysis of wheat leaf and root tissues treated with different concentrations of IAA (0, 1, and 50 μM). …”
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Tumor-agnostic transcriptome-based classifier identifies spatial infiltration patterns of CD8+T cells in the tumor microenvironment and predicts clinical outcome in early-phase and... by Cláudia S Ferreira, Konstanty Korski, Michael A Cannarile, Irina Klaman, Petra C Schwalie, Iakov I Davydov, Andreas Roller, Martha L Serrano-Serrano, Astrid Heller, Nicolas Staedler, Gabriele Dietmann, Alberto Valdeolivas

“…A good correspondence between the transcriptome and the IHC-based evaluation enabled us to develop a 92-gene classifier that accurately predicted the IHC-based CD8 immunophenotype in primary and metastatic samples (area under the curve inflamed=0.846; excluded=0.712; desert=0.855). …”
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Effects of Training Systems on Sugar Accumulation and Metabolism in ‘Kyoho’ Grape Berries by Xinming Liu, Jinhui Lin, Ting Chen, Keyang Chen, Yan Lei

“…Fruit samples were collected from 45 to 95 days after flowering (DAF) to measure soluble sugar content. Transcriptome sequencing was performed to analyze the differential expression of sugar metabolism-related genes, combined with KEGG enrichment analysis and RT-qPCR validation of key genes. …”
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Unraveling the Nectar Secretion Pathway and Floral-Specific Expression of <i>SWEET</i> and <i>CWIV</i> Genes in Five Dandelion Species Through RNA Sequencing by Sivagami-Jean Claude, Sunmi Park, Seong-Jun Park, SeonJoo Park

“…<i>Taraxacum</i>, a genus in the Asteraceae family, is widely distributed across temperate regions and plays a vital ecological role by providing nectar and pollen to pollinators during the early flowering season. …”
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Identification of regulatory loci and candidate genes related to body weight traits in broilers based on different models by Na Luo, Keqi Cai, Limin Wei, Huanxian Cui, Jie Wen, Bingxing An, Guiping Zhao

“…These overlapping SNPs represent robust loci that may influence both traits across different statistical approaches. Transcriptome sequencing indicated differential expression of LDB2 and SEL1L3 between high and low BW groups. …”
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Courtship Is a Major Factor of Mating‐Shortened Male Lifespan in an Egg Parasitoid by Zi‐Yin Wang, Jing Li, Jia‐Min Tang, Lan‐Feng Qiu, Hao‐Yuan Hu, Peng‐Cheng Liu

“…In summary, our study provides comprehensive insights into post‐mating changes in male longevity and provides a basis for future mechanistic studies.…”
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Optimizing Cost-Effective gene expression phenotyping approaches in cattle using 3′ mRNA sequencing by Ruwaa I. Mohamed, Taylor B. Ault-Seay, Sonia J. Moisá, Jonathan E. Beever, Agustín G. Ríus, Troy N. Rowan

“…However, progressively more reads did provide marginal increases in recall across metrics. …”
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Fluridone promotes the germination of Polygonatum cyrtonema seeds by modulating hormone signal transduction, phenylpropanoid biosynthesis, and energy metabolism by Xiaogang Jiang, Darong Li, Hua Wang, Yuying Yang, Kaidi Yu, Jinwen You, Haihua Liu, Xiaoliang Guo, Yinsheng He, Wuxian Zhou, Qingfang Wang

“…In addition, we investigated the metabolome and transcriptome differences in P. cyrtonema seed under fluridone treatments of 0 mg/L (CK), 50 mg/L (FL5), and 250 mg/L (FL20). …”
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Arsenic sulfide alleviates the progression of liver cancer malignancy by inhibiting the expression of TLCD1 in mice by Xianglu Li, Xuehua Xing, Lin Wang, Shizong Li

“…This study provides a molecular basis for arsenic sulfide in the treatment of liver cancer.…”
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Extraction of a stromal metastatic gene signature in breast cancer via spatial profiling by Giorgio Bertolazzi, Valeria Cancila, Davide Vacca, Beatrice Belmonte, Daniele Lecis, Parsa Sirati Moghaddam, Arianna Di Napoli, Mario Paolo Colombo, Giancarlo Pruneri, Giannino Del Sal, Giorgio Scita, Matteo Fassan, Andrea Vecchione, Silvio Bicciato, Claudio Tripodo

“…We identified a stromal metastatic (Met) signature, which was subsequently validated across transcriptomic reference human breast cancer (BC) datasets and in spatial transcriptomics of a murine model. …”
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Seasonal dynamics and molecular regulation of flavonoid biosynthesis in Cyclocarya paliurus (Batal.) Iljinsk by Duo Chen, Yixin Xiao, Xuehai Zheng, Huamiao Sun, Cifeng Zhang, Jinmao Zhu, Ting Xue

“…Understanding the seasonal dynamics and molecular regulation of flavonoid biosynthesis in this species is crucial for optimizing its production.MethodsWe conducted an integrated analysis of transcriptomic and metabolomic data to identify key genes involved in flavonoid biosynthesis and regulation. …”
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