Decoding mitochondrial stress genes in DCM: towards precision diagnosis and therapy by Bingbing Zhu, Hai Cheng, Jiawei Li, Yangyang Hu, Xiaoning Ge

“…Methods We sourced transcriptomic data from the GEO database and mitochondrial oxidative stress-related genes from GeneCards. …”
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The impact of dropouts in scRNAseq dense neighborhood analysis by Alisa Pavel, Manja Gersholm Grønberg, Line H. Clemmensen

“…Single cell RNA sequencing (scRNAseq) provides the possibility to investigate transcriptomic profiles on a single cell level. However, the data show unique challenges in comparison to bulk transcriptomic data, one being high dropout rates, which yields high sparsity data. …”
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Multifactor transcriptional profiling of potato during 2,4-D-induced resistance to common scab disease by Matthew L. Fabian, Hien P. Nguyen, John R. Stommel, Christopher R. Clarke

“…Pathogen infection primarily altered transcriptomic responses in tuber periderm tissue, while foliar 2,4-D application caused larger shifts in gene expression in leaf tissue, as expected. …”
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iPSCs and iPSC-derived cells as a model of human genetic and epigenetic variation by Kara Quaid, Xiaoyun Xing, Yi-Hsien Chen, Yong Miao, Amber Neilson, Vijayalingam Selvamani, Aaron Tran, Xiaoxia Cui, Ming Hu, Ting Wang

“…We propose that human induced Pluripotent Stem Cells (iPSCs) are an excellent model to study the relationship between genetic and epigenetic variation while controlling for environmental factors. In this study, we have created a comprehensive resource of high-quality genomic, epigenomic, and transcriptomic data from iPSC lines and three iPSC-derived cell types (neural stem cell (NSC), motor neuron, monocyte) from three healthy donors. …”
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Multiple Omics Analyses Reveal Activation of Nitrogen Metabolism and Flavonoid Glycosylation in <i>Toxicodendron vernicifluum</i> Under High Temperature by Guoqing Bai, Ruiwen Ding, Qizhen Su, Xiaomin Ge, Shasha Li, Huiying Shang, Aiguo Zhao, Chen Chen

“…Indole-3-acetic acid remained stable while abscisic acid decreased, with increases in jasmonic acid and jasmonoyl-L-isoleucine indicating complex hormonal responses. …”
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Brown adipose tissue-derived extracellular vesicles regulate hepatocyte mitochondrial activity to alleviate high-fat diet-induced jawbone osteoporosis in mice by Kai Zhang, Kai Zhang, Sha Zhang, Sha Zhang, Sha Zhang, Guorong Deng, Guangxiang He, Guangxiang He, Yuan Yuan, Yu Fu, Yihan Liu, Zhen Gong, Liang Kong, Chenxi Zheng

“…The use of metabolic regulators represents a promising therapeutic strategy for OP management. While brown adipose tissue-derived extracellular vesicles (BEV) exhibit metabolic regulatory potential, their capacity to mitigate LMD-associated OP remains unclear.MethodsA high-fat diet (HFD)-induced LMD mouse model was established to identify the JOP phenotype through micro-computed tomography (micro-CT) and transcriptomic profiling. …”
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Comprehensive profiling of extrachromosomal circular DNAs in colorectal cancer progression by Lu Lu, Mingjie Chen, Guicheng Zhang, Yujing Liu, Xiangyuan Xu, Zenghua Jiang, Yangxian Xu, Tao Liu, Fan Yang, Guang Ji, Hanchen Xu

“…Using Circle-Sequencing and whole transcriptomic sequencing, we comprehensively profile circular DNAs and transcriptomes in healthy individuals, colorectal adenoma, and CRC patients. …”
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Haplotype-resolved T2T genome assembly of the pear cultivar ‘Danxiahong’ by Xiangzhan Zhang, Jianxin Bian, Yanan Wang, Lei Wang, Long Wang, Suke Wang, Yanli Su, Hang He, Huabai Xue

“…The haplotype-resolved genome of ‘Danxiahong’ significantly contributes to the investigation of genes and molecular mechanisms related to fruit quality, while also facilitating the Multi-Omics analysis, such as comparative genomics, transcriptomics, proteomics, and allelic expression research.…”
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The mechanotransducer Piezo1 coordinates metabolism and inflammation to promote skin growth by Yingchao Xue, Elizabeth Winnicki, Zhaoxu Zhang, Ines Lopez, Saifeng Wang, Charles Kirby, Sam S. Lee, Ang Li, Chaewon Lee, Hana Minsky, Kaitlin Williams, Kevin Yueh-Hsun Yang, Ling He, Sashank K. Reddy, Luis A. Garza

“…Additionally, skin expansion increases macrophage and monocyte infiltration in the skin while altering systemic immune cell profiles. Glycolysis-related genes, including Glut1 and Aldoa were significantly elevated. …”
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The phosphatase CTDSPL2 promotes proliferation, invasion, metastasis and regorafenib resistance in osteosarcoma by Guannan Bai, Shaobo Zhao, Manli Zhao, Limiao Chen, Wenhao Chen

“…The mechanisms associated with regorafenib resistance remains unclear.In this study we performed transcriptomics, proteomics and phosphorylated proteomics using regorafenib-treated osteosarcoma cell lines (MG-63, HOS-MNNG for transcriptomics, HOS-MNNG for proteomics and phosphorylated proteomics). …”
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Lysosomal free sialic acid storage disorder iPSC-derived neural cells display altered glycosphingolipid metabolism by Marya S. Sabir, Vukasin M. Jovanovic, Seungmi Ryu, Chaitali Sen, Pinar Ormanoglu, Laura Pollard, Richard Steet, William A. Gahl, Marjan Huizing, Carlos A. Tristan, Frances M. Platt, May Christine V. Malicdan

“…Abstract Lysosomal free sialic acid storage disorder (FSASD) is a rare neurodegenerative disease caused by biallelic mutations in SLC17A5, encoding the lysosomal sialic acid exporter, SLC17A5 (sialin). While the involvement of oligodendroglia in FSASD pathogenesis is established, the roles of other neural cell types remain elusive. …”
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Genome-Wide Analysis of GmMYB S20 Transcription Factors Reveals Their Critical Role in Soybean Nodulation by Junchen Leng, Ruobing Xu, Yanshuang Liu, Tianshu Jiang, Haiying Hu, Zhaojun Ding, Shaojun Dai

“…Functional analyses revealed that loss of <i>GmMYB62s</i> function significantly reduced nodule density, while overexpression promoted nodulation. Transcriptomic analysis (RNA-seq) further demonstrated that <i>GmMYB62s</i> regulate key pathways, including hormone signaling, immune responses, and cell wall metabolism, thereby coordinating symbiotic interactions. …”
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Polysaccharides derived from Rosa rugosa cv. Plena ameliorate colorectal cancer by regulating intestinal microbiota composition and lipid metabolism pathway by Chunyu Dai, Xuan Zheng, Jingxin Zhu, Hongxing Zhang, Junhua Jin, Xiaona Pang, Xiangyang Li, Yuanhong Xie

“…In CRC mice, RPP1 administration reduced colonic polyp formation and ameliorated colon shortening while normalizing elevated serum IL-1β and TNF-α levels. …”
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Exploring the Skin Benefits of Extremophilic Postbiotics from <i>Exiguobacterium artemiae</i>: A New Frontier in Thermal Protection by Haeun Lee, Dayeon Roo, Dong-Geol Lee, Seunghyun Kang, Jinwoo Min, Heecheol Kang, Young Mok Heo, Kyung Eun Lee

“…Rising global temperatures increase skin exposure to heat stress, which can impair skin structure and function. While several cosmetic ingredients have been developed to mitigate heat-induced damage, most primarily aim to enhance hydration or suppress inflammation, lacking mechanistic insights into their action under heat stress. …”
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Integrative Multiomics Profiling of Mouse Hippocampus Reveals Transcriptional Upregulation of Interferon‐Stimulated Genes Through PU.1 Regulator in Microglial Activation Induced by... by Zengyu Zhang, Dewen Ru, Zhuohang Liu, Zimin Guo, Lei Zhu, Yuan Zhang, Min Chu, Yong Wang, Jing Zhao

“…Behavioral assessments revealed cognitive impairments, while neuropathological analysis confirmed hippocampal damage. …”
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Evaluation of Metabolic Characteristics Induced by Deoxynivalenol in 3D4/21 Cells by Yu Han, Bo Yu, Wenao Weng, Liangyu Shi, Jing Zhang

“…Integration with transcriptomic data confirmed that these pathways play key roles in DON-induced immunotoxicity. …”
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Fungal Coculture: Unlocking the Potential for Efficient Bioconversion of Lignocellulosic Biomass by Rafael Icaro Matos Vieira, Alencar da Silva Peixoto, Antonielle Vieira Monclaro, Carlos André Ornelas Ricart, Edivaldo Ximenes Ferreira Filho, Robert Neil Gerard Miller, Taísa Godoy Gomes

“…This approach to biomass conversion offers potential for enhancing production of enzymes, biofuels, and other high-value bioproducts, while enabling investigation of ecological dynamics and metabolic pathways relevant to biorefinery operations. …”
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Behavioral assessment and gene expression changes in a mouse model with dysfunctional STAT1 signaling by Luca Büschgens, Nina Hempel, Aditi Methi, Andre Fischer, Nele Siering, Lars Piepkorn, Olaf Jahn, Thomas Meyer, Oliver Wirths

“…Methods Here, we characterized a STAT1 targeted-disruption mouse model in the absence of infectious stimuli by employing established behavioral testing paradigms and immunohistochemical stainings, as well as bulk hippocampal transcriptomic and proteomic analyses. Results While we found neither overt behavioral alterations nor immunohistochemical changes with respect to microglial phagocytosis or proliferation, significant alterations were detected in gene and protein expression profiles implicated in neuroinflammatory processes and neuroprotection. …”
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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

“…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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FBXO10 Drives Hepatocellular Carcinoma Proliferation via K63-Linked Ubiquitination and Stabilization of FRMPD1 by Wuguang Liu, Bin Xu, Kashif Kifayat, Yuhong Xie, Xiaolong Liu, Chengyong Dong, Liming Wang

“…Functionally, FBXO10 silencing suppressed HCC cell proliferation while its overexpression promoted tumor growth. Mechanistic studies revealed that FBXO10 directly interacts with FRMPD1 to mediate its K63-linked polyubiquitination and stabilization, independent of transcriptional regulation. …”
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