Evaluation of Metabolic Characteristics Induced by Deoxynivalenol in 3D4/21 Cells by Yu Han, Bo Yu, Wenao Weng, Liangyu Shi, Jing Zhang

“…Principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA) revealed distinct metabolic profiles between control and DON-treated groups. …”
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Sleep deprivation impacts the immunological milieu of epididymis leading to low sperm quality in rats by Zhean Li, Shengnan Gong, Ziqi Yu, Yujia Luo, Yixiang Zhao, Erfei Xue, Huimin Lu, Di Xiang, Fei Sun

“…SD treatment also decreases serum testosterone levels and epididymal sperm transit time in male rats. Histological analysis reveals reproductive system damage, while bulk and single-cell RNA sequencing highlight that SD significantly alters transcriptomes and induces differentially expressed genes with significant heterogeneity across three segments of the epididymis. …”
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Immune Characters and Plasticity of the Sentinel Lymph Node in Colorectal Cancer Patients by Xiaoyun Li, Jingling Tang, Hang Du, Xinjun Wang, Liyun Wu, Pingsheng Hu, Hua Zhang, Ruyi Zhang, Yuan Yang

“…Differential expression and distribution of characteristic immune cell markers were analyzed by multiplex immunohistochemistry (mIHC). Transcriptomics analysis was conducted to compare the differences in the expression of immune-related genes among lymph nodes. …”
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Identification of critical transition signal (CTS) to characterize regulated stochasticity during ABA-induced growth-to-defense transition by Rasmieh Hamid, Bahman Panahi, Feba Jacob, Amir Ghaffar Shahriari

“…Gene Ontology (GO) enrichment analysis revealed a significant overrepresentation of defense-related biological processes, while STRING network analysis revealed strong functional interactions between DNB genes and differentially expressed genes (DEGs) and highlighted key regulatory hubs. …”
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Druggable genome-wide Mendelian randomization integrating GWAS and eQTL/pQTL data identifies targets for lung squamous cell carcinoma by Shizhao Cheng, Hao Zhang, Zhenliang Shi, Daqiang Sun

“…Bayesian co-localization analysis, summary‑data‑based MR (SMR) analysis, and HEIDI test were conducted to verify the causal associations between genes and LUSC risk. …”
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Transcriptions of ACO and ACS genes are involved in nitrate-dependent root growth of maize seedlings by Guoqi Yao, Zhenwei Yan, Shijun Ma, Xia Liu, Juan Shan, Bing Cao, Xiaole Chen, Bingying Leng, Chunhua Mu

“…In this research, we performed Gene Set Enrichment Analysis (GSEA) of maize transcriptomes in response to nitrate and found that the ethylene action pathway might participate in nitrate signaling. …”
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Identification and Characterization of SQUAMOSA Promoter Binding Protein-like Transcription Factor Family Members in <i>Zanthoxylum bungeanum</i> and Their Expression Profiles in R... by Shengshu Wang, Weiming Hu, Xueli Zhang, Yulin Liu, Fen Liu

“…This study used transcriptomic and bioinformatics data to conduct a thorough genomic identification and expression investigation of the <i>ZbSPL</i> gene family. …”
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RNAseq and targeted metabolomics implicate RIC8 in regulation of energy homeostasis, amino acid compartmentation, and asexual development in Neurospora crassa by Monique Quinn, Alexander J. Carrillo, Lida Halilovic, Katherine A. Borkovich

“…RNAseq analysis showed that the Δgna-1 mutant possesses 159 mis-regulated genes, while Δgna-3 and Δric8 strains have more than 1,000 each. …”
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Switch-like gene expression modulates disease risk by Alber Aqil, Yanyan Li, Zhiliang Wang, Saiful Islam, Madison Russell, Theodora Kunovac Kallak, Marie Saitou, Omer Gokcumen, Naoki Masuda

“…Abstract While switch-like gene expression (“on” in some individuals and “off” in others) has been linked to biological variation and disease susceptibility, a systematic analysis across tissues is lacking. …”
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Distinct immune responses to proton and photon radiotherapy: implications for anti-PD-L1 combination therapy in colorectal cancer by Hélène Burckel, Anaïs Nicol, Carole Mura, Marc Rousseau, Jolie Bou-Gharios, Lisa Froidurot, Corentin Richard, Véronique Morgand, Pierre-Antoine Laurent, Emeric Limagne, Romain Boidot, Georges Noël, Céline Mirjolet

“…Seven days post-treatment, transcriptomic analysis and immune response assessments to characterize lymphoid cells, myeloid cells, and PD-L1 expression were performed. …”
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SPINK1 facilitates tumor progression via the EGFR/JAK/STAT3 axis in oral squamous cell carcinoma: insights from single-cell RNA sequencing by Mingyan Bao, Zhangui Tang

“…Cell-cell communication networks were reconstructed to map ligand-receptor interactions, while Gene Set Variation Analysis (GSVA) and Gene Set Enrichment Analysis (GSEA) were employed to systematically investigate SPINK1-associated signaling pathways. …”
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SHMT inhibitor synergizes with 5-Fu to suppress gastric cancer via cell cycle arrest and chemoresistance alleviation by Huan Deng, Yajie Wang, Lin Xiao, Mei Feng, Weidong Dou, Yisheng Pan

“…Drug synergistic screening assays were used to build the therapeutic model in the study. The transcriptomic analysis was performed to clarify the underlying mechanism of combination treatment. …”
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Machine learning explores the prognostic and immuno-oncological impact of mitochondrial unfolded protein response in CESC by Keh-Sen Liu, Yen-Hsiang Chang, Hsing-Ju Wu, Hung-Yu Lin

“…Methods We employed machine learning to analyze UPRmt genes in CESC using TCGA multi-omics data. Our comprehensive analysis included genetic alterations, prognostic significance, tumor-immune interactions, single-cell transcriptomics, pathway enrichment, and drug sensitivity assessments. …”
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Genetic gradual reduction of OGT activity unveils the essential role of O-GlcNAc in the mouse embryo. by Sara Formichetti, Agnieszka Sadowska, Michela Ascolani, Julia Hansen, Kerstin Ganter, Christophe Lancrin, Neil Humphreys, Mathieu Boulard

“…We identified hypomorphic Ogt alleles that perturb O-GlcNAc homeostasis while being compatible with embryogenesis. The analysis of the transcriptomes of the mutant embryos at different developmental stages suggested a sexually-dimorphic developmental delay caused by the decrease in O-GlcNAc. …”
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Live Malassezia strains from the mucosa of patients with ulcerative colitis: pathogenic potential and environmental adaptations by Yong-Joon Cho, Seung Yong Shin, Juan Yang, Hyo Keun Kim, Piyapat Rintarhat, Minji Park, Muhyeon Sung, Kate Lagree, David M. Underhill, Dong-Woo Lee, Sohyeong Choi, Chang Hwan Choi, Chul-Su Yang, Won Hee Jung

“…While both gut and skin isolates of M. globosa shared high genomic similarity, transcriptomic analysis revealed distinct responses to oxygen levels, suggesting niche-specific adaptation. …”
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Oxygen Regulates Human Pluripotent Stem Cell Metabolic Flux by Jarmon G. Lees, Timothy S. Cliff, Amanda Gammilonghi, James G. Ryall, Stephen Dalton, David K. Gardner, Alexandra J. Harvey

“…RNA-seq analysis of 5% oxygen hPSC also indicated increases in glycolysis, lysine demethylases, and glucose-derived carbon metabolism, while increased methyltransferase and cell cycle activity was indicated at 20% oxygen. …”
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Biventricular electromechanical dysfunction and molecular remodeling in a rat model of advanced pulmonary arterial hypertension by Francesco Paolo Lo Muzio, Alessia Caputo, Rosario Statello, Mirko Hu, Roberta Maestri, Giovanna Pelà, Aderville Cabassi, Margherita Burattini, Giacomo Rozzi, Silvia Berrettoni, Barbara Montanini, Stefano Rossi, Lorenzo Fassina, Giovanni Battista Luciani, Gianluigi Condorelli, Michele Miragoli

“…In the LV, PAH also results in increased refractoriness from 95.4 ± 3.0 ms to 140.0 ± 11.5 ms and reduced transverse conduction velocity by 14%, despite preserved EF. Transcriptomic analysis indicates that while both ventricles exhibit upregulation of extracellular matrix remodeling-related genes, the RV primarily shows downregulation of electromechanical-related genes. …”
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Residual cell types, molecular expression profiles and quality assessment of in vitro cultured human thymic slices by GUAN Wanqing, LUO Guihua, HAN Jingxuan

“…Flow cytometry and histologic analysis were utilized to observe the immune reconstitution after transplantation. …”
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Single-Cell Atlas of Spleen Remodeling Reveals Macrophage Subset-Driven ASFV Pathogenesis by Liyuan Wang, Shouzhang Sun, Lei Liu, Yun Chen, Haixue Zheng, Zhonglin Tang

“…Viral gene expression analysis revealed E165R as a central hub in viral replication networks, while host transcriptomics uncovered disruption of Netrin signaling pathways that may facilitate immune evasion. …”
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A R1-type MYB CmREVEILLE2 regulates light-mediated chlorophyll biosynthesis and green color formation in chrysanthemum flowers by Jingjie Fang, Sitong Liu, Sijia Chen, Huijie Deng, Linxia Zhao, Xinwei Liang, Ziqiang Chen, Xiaoqin Zhang, Songwen Xu, Caiyun Wang, Jing Luo

“…A R1-type MYB transcription factor, CmREVEILLE2 (CmRVE2), was identified through transcriptomic analysis of flowers subjected to different light intensities (3,000 Lux for low light, LL; 6,000 Lux for moderate light, ML; and 12,000 Lux for high light, HL). …”
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