Transcriptomic Analysis of Menstrual Blood-Derived Stem Cells Transplantation Combined with Exercise Training in Promoting Spinal Cord Injury Recovery in Rats by QI Longju, CHEN Shiyuan, LIAO Zehua, SHI Yuanhu, SUN Yuyu, WANG Qinghua

“…Spinal cord tissue from the injury site was selected for transcriptome sequencing, and mRNA expression data from both the SCI and CTMT groups were analyzed. Differential gene expression, GO (Gene Ontology) functional enrichment, KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment, and protein-protein interaction (PPI) network analyses were performed. …”
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Exploring the CD3/CD56/TNF-α/Caspase3 pathway in pyrethroid-induced immune dysregulation: curcumin-loaded chitosan nanoparticle intervention by Nawal Alsubaie, Yasmina M. Abd-Elhakim, Amany Abdel-Rahman Mohamed, Tarek Khamis, Tarek Khamis, Mohamed M. M. Metwally, Mohamed M. M. Metwally, Nawal Helmi, Afnan M. Alnajeebi, Badriyah S. Alotaibi, Amirah Albaqami, Wedad Mawkili, Mai A. Samak, Mai A. Samak, Samar A. Eissa

“…However, the alterations in immune function, splenic antioxidant status, blood cell populations, and immune-related gene expression were notably restored in the FTN + CML-CNP-treated group.ConclusionThe findings of this study highlighted the immunosuppressive effects of FTN and suggested the involvement of many CD cell markers as a potential underlying mechanism. …”
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Epigenetic modifications in bladder cancer: crosstalk between DNA methylation and miRNAs by Wei Li, Wei Li, Wei Li, Peiyue Luo, Peiyue Luo, Peiyue Luo, Qi Chen, Qi Chen, Qi Chen, Le Cheng, Le Cheng, Le Cheng, Lifeng Gan, Lifeng Gan, Lifeng Gan, Fangtao Zhang, Fangtao Zhang, Fangtao Zhang, Haidong Zhong, Haidong Zhong, Haidong Zhong, Liying Zheng, Biao Qian, Biao Qian

“…These modifications not only affect gene expression but also impact critical biological behaviors of tumor cells, including proliferation, differentiation, apoptosis, invasion, and metastasis. …”
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Generation of live mice from haploid ESCs with germline-DMR deletions or switch by Yongjian Ma, Meng Yan, Zhenfei Xie, Hongling Zhang, Zhoujie Li, Yuanyuan Li, Suming Yang, Meiling Zhang, Wen Li, Jinsong Li

“…Moreover, embryos reconstructed by injection of AG-haESCs with hypomethylated H19-DMR into oocytes with H19-DMR deletion develop into live mice sustaining inverted allelic gene expression. Together, our findings indicate that restoration of monoallelic expression of 10 imprinted regions is adequate for the full-term development of all-haESC pups, and it works irrespective of their parental origins. …”
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Hypothyroidism impairs the circadian rhythmicity of clock genes and proteins involved in gut nutrient absorption in female mice by Ayla Secio-Silva, Paulo Henrique Evangelista-Silva, Felipe Emrich, Letícia Selvatici-Tolentino, Maíza Ferreira, Ana Bárbara de Paula Silva, Bruno Henrique Gomes, Tatienne Neder Figueira-Costa, André Gustavo Oliveira, Rodrigo Antonio Peliciari-Garcia, Francemilson Goulart-Silva, Paula Bargi-Souza

“…The proximal small intestine segment was collected and immediately frozen for gene expression analysis of circadian core clock components (Bmal1, Per2, Cry1, and Nr1d1) and nutrient transporters by RT-qPCR. …”
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MiR-3664-3p through suppressing ABCG2, CYP3A4, MCL1, and MLH1 increases the sensitivity of colorectal cancer cells to irinotecan by Elham Farrokhnazar, Sahar Moghbelinejad, Reza Najafipour, Ladan Teimoori-Toolabi

“…When we transfected HCT116-R3 and SW480-R3 cells with pre-miR-3664-3p, there was an increase in miR-3664-3p expression and a reduction in ABCG2, CYP3A4, MCL1, and MLH1 gene expression. This led to increased sensitivity to irinotecan. …”
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Comprehensive analysis of scRNA-seq and bulk RNA-seq reveals the non-cardiomyocytes heterogeneity and novel cell populations in dilated cardiomyopathy by Siyu He, Chunyu Li, Mingxin Lu, Fang Lin, Sangyu Hu, Junfang Zhang, Luying Peng, Li Li

“…Further analysis revealed high heterogeneity in tissue preference, gene expression, functional enrichment, immunodynamics, transcriptional regulatory factors, metabolic changes, and communication patterns in fibroblasts and myeloid cells. …”
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SSL5-AnxA5 Fusion Protein Constructed Based on Human Atherosclerotic Plaque scRNA-Seq Data Preventing the Binding of Apoptotic Endothelial Cells, Platelets, and Inflammatory Cells by Yifei Zhao, Xingyu He, Teng Hu, Tianli Xia, Fangyang Huang, Changming Li, Yiming Li, Fei Chen, Mao Chen, Jun Ma, Yong Peng

“…<b>Methods:</b> The scRNA-seq data were extracted from the Gene Expression Omnibus (GEO) database. Single-cell transcriptome analysis results and cell–cell communication were analyzed to identify the ACS and SAP cell clusters and elucidate the intercellular communication differences. …”
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A pan-cancer analysis of homeobox family: expression characteristics and latent significance in prognosis and immune microenvironment by Yuanhui Wang, Jie Gao, Ziyi Ren, Ziyi Shen, Wei Gu, Qinyi Miao, Xiaomeng Hu, Xiaomeng Hu, Yan Wu, Yan Wu, Wei Liu, Jia Jia, Jia Jia, Yi Cai, Chunpeng (Craig) Wan, Lei Sun, Tingdong Yan, Tingdong Yan

“…Potential anti-tumor compounds for down-regulating HOX gene expression were identified, such as HDAC inhibitors and tubulin inhibitors. …”
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Role of sphingolipid metabolism signaling in a novel mouse model of renal osteodystrophy based on transcriptomic approach by Yujia Wang, Yan Di, Yongqi Li, Jing Lu, Bofan Ji, Yuxia Zhang, Zhiqing Chen, Sijie Chen, Bicheng Liu, Rining Tang, Yuanyuan Ji

“…RNA-seq was utilized to profile gene expression changes of ROD. We elucidated the functions of differentially expressed genes (DEGs) using gene ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and gene set enrichment analysis (GSEA). …”
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The transcriptional analysis of pepper shed light on a proviral role of light-harvesting chlorophyll a/b binding protein 13 during infection of pepper mild mottle virus by Weihong Lin, Shugen Zhang, Hao Zhang, Xiaomei Deng, Tong Jiang, Xifeng Chen, Laihua Dong, Qin Yan, Lianyi Zang, Yongping Xing, Zhenquan Wang, Qin Zhang, Kaitong Du, Huolin Shen, Junmin Zhang, Tao Zhou

“…Taken together, our findings highlight the distinct gene expression profiles between susceptible and resistant pepper lines in response to PMMoV infection and confirm the proviral role of CAB13. …”
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IFN-γ reprograms cardiac microvascular endothelial cells to mediate doxorubicin transport and influences the sensitivity of mice to doxorubicin-induced cardiotoxicity by Haoyu Ji, Wenya Ma, Xu Liu, Hongyang Chen, Yining Liu, Zhongyu Ren, Daohong Yin, Ao Cai, Zizhen Zhang, Xin Wang, Wei Huang, Leping Shi, Yanan Tian, Yang Yu, Xiuxiu Wang, Yang Li, Yu Liu, Benzhi Cai

“…Single-cell RNA sequencing revealed differences of gene expression in cardiac endothelial cells between DIC-insensitive and DIC-sensitive groups. …”
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Effects of dietary amylose/amylopectin ratio on antioxidant ability and amino metabolism in the liver of weaned piglets undergoing feed transition and challenged with lipopolysacch... by Can Yang, Can Yang, Xiaowu Tang, Min Wang, Han Yang, Huansheng Yang, Yancan Wang, Yulong Yin, Yulong Yin

“…There was significant effect of LPS stress * dietary DAR on total SOD activity and SOD1 mRNA gene expression (p &lt; 0.05), LPS stress caused an increase in those two indices for pigs in groups 0.00 and 0.80. …”
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Efficacy of the Bushen Jianpi Huoxue Formula on Beclin-1/Bcl-2-mediated autophagy and apoptosis in osteoblasts by Yanping Lin, Yanping Lin, Rui Zhao, Rui Zhao, Jiachun Huang, Tongying Chen, Tongying Chen, Haolin Yang, Haolin Yang, Haiwei Guo, Lei Wan, Zhihai Zhang, Ying Li, Genfu Zhu, Hongxing Huang, Hongxing Huang

“…Beclin-1 overexpressed osteoblasts were constructed by transfection. Gene expression and protein level were examined by qRT-PCR and immunoblotting assay. …”
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Metformin blocks BIK1-mediated CPK28 phosphorylation and enhances plant immunity by Yazhou Bao, Qian Zhang, Hai Zhu, Yong Pei, Yaning Zhao, Yixin Li, Peiyun Ji, Dandan Du, Hao Peng, Guangyuan Xu, Xiaodan Wang, Zhiyuan Yin, Gan Ai, Xiangxiu Liang, Daolong Dou

“…Methods: To investigate the impact of MET on enhancing plant immune responses, we conducted assays measuring defense gene expression, reactive oxygen species (ROS) accumulation, mitogen-activated protein kinase (MAPK) phosphorylation, and pathogen infection. …”
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Microglia depletion reduces neurodegeneration and remodels extracellular matrix in a mouse Parkinson’s disease model triggered by α-synuclein overexpression by Zhen Zhang, Kun Niu, Taoying Huang, Jiali Guo, Gongbikai Xarbat, Xiaoli Gong, Yunke Gao, Feiyang Liu, Shan Cheng, Wenting Su, Fei Yang, Zhaoyuan Liu, Florent Ginhoux, Ting Zhang

“…This chronic treatment paradigm prevented the development of motor deficits and concomitantly preserved dopaminergic neuron cell and weakened α-synuclein phosphorylation. Gene expression profiles related to extracellular matrix (ECM) remodeling were increased after microglia depletion in PD mice, which were further validated on protein level. …”
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Single-cell immunopathology of recurrent acute generalized exanthematous pustulosis associated with vancomycin by Eric M. Mukherjee, MD, PhD, Andrew Gibson, PhD, Matthew S. Krantz, MD, Rama Gangula, MS, Amy M. Palubinsky, PhD, Alan S. Boyd, MD, Jeffrey P. Zwerner, MD, PhD, Anna K. Dewan, MD, MS, Nontaya Nakkam, PhD, Katherine C. Konvinse, MD, PhD, Yueran Li, PhD, Ramesh Ram, PhD, Abha Chopra, PhD, Elizabeth J. Phillips, MD

“…Single-cell analysis of affected skin showed polyclonal TH17-like cells with gene expression signatures similar to T-cell response during prevalent infectious diseases. …”
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Regulatory signatures involved in the cell cycle pathway contribute to egg production heterosis in chicken by Jingwei Yuan, Yuanmei Wang, Yanyan Sun, Yunlei Li, Aixin Ni, Qin Li, Hanhan Yang, Xinying Xu, Yunhe Zong, Hui Ma, Jilan Chen

“…Conclusion Our study characterized the dynamic profile of genome-wide gene expression in ovary and highlighted the role of dominant expression of cell cycle pathway genes in heterosis. …”
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Genome-wide analysis of sugar transporter gene family in Erianthus rufipilus and Saccharum officinarum, expression profiling and identification of transcription factors by Sehrish Akbar, Xuiting Hua, Yingying Zhang, Gang Liu, Tianyou Wang, Huihong Shi, Zhen Li, Yiying Qi, Habiba Habiba, Wei Yao, Mu-Qing Zhang, Jisen Zhang

“…In this study, we performed genome wide and gene expression data analysis to identify the putative ST genes in Erianthus rufipilus (E. rufipilus) and in Saccharum officinarum (S. officinarum). …”
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Integrating pharmacogenomics and cheminformatics with diverse disease phenotypes for cell type-guided drug discovery by Arda Halu, Sarvesh Chelvanambi, Julius L. Decano, Joan T. Matamalas, Mary Whelan, Takaharu Asano, Namitra Kalicharran, Sasha A. Singh, Joseph Loscalzo, Masanori Aikawa

“…We benchmark our approach by calculating area under the receiver operating characteristic curves (AUROC) for 73 gene sets from the Molecular Signatures Database (MSigDB) using target gene expression profiles from the Comparative Toxicogenomics Database (CTD). …”
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