The landscape of RNA 5-methylcytosine modification during chicken embryonic myogenesis by Hongxia Jiang, Jing Liu, Yuxiang Wang, Zurong Liao, Xiaoyun Xiao, Zhenxvan Ding, Xvwen Huang, Wenwei Li, Zikun Wang, Jingzhan Liang, Jiguo Xu, Xiaolong Hu, Huirong Mao, Sanfeng Liu, Biao Chen

“…Our results indicate that m5C modifications are widespread in chicken skeletal muscle transcriptome and present a unique distribution pattern. …”
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Quantitative-proteomic comparison of alpha and Beta cells to uncover novel targets for lineage reprogramming. by Amit Choudhary, Kaihui Hu He, Philipp Mertins, Namrata D Udeshi, Vlado Dančík, Dina Fomina-Yadlin, Stefan Kubicek, Paul A Clemons, Stuart L Schreiber, Steven A Carr, Bridget K Wagner

“…To identify potential lineage reprogramming protein targets, we compared the transcriptome, proteome, and phosphoproteome of alpha cells, beta cells, and compound-treated alpha cells. …”
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Distinct mechanisms of electroacupuncture and manual acupuncture in modulating hypothalamic GnRH–tanycyte unit function of polycystic ovary syndrome by Yu Wang, Yicong Wang, Yuning Chen, Wenhan Lu, Xiaoyu Tong, Jiajia Li, Wenhao Gao, Rui Huang, Wei Hu, Yi Feng

“…These findings highlight potential hypothalamic targets and provide new insights into the distinct mechanisms of EA and MA.…”
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Effects of RNA m6A on the formation of multi-petalization in Magnolia wufengensis: Mechanistic insights and gene expression analysis by Cunjie Li, Huarong Li, Jiang Ma, Xiaoning Fan, Yanjun Cai, Liyuan Chen, Hanlin Zhou, Hongwei Liang, Chao Zhou, Faju Chen

“…N6-Methyladenosine (m6A) is the most common modification in the transcriptome of biological RNA and plays roles that include maintaining the stability and transportation of mRNA, mRNA precursor shearing, polyadenylation, and the initiation of translation. …”
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Single-Cell Analysis Reveals the Cellular and Molecular Changes of Liver Injury and Fibrosis in Mice During the Progression of <i>Schistosoma japonicum</i> Infection by Julu Lu, Xinyue Zhang, Panpan Dong, Congjin Mei, Yingying Yang, Chuanxin Yu, Lijun Song

“…In addition, scRNA-seq and quantitative reverse transcription polymerase chain reaction (qRT-PCR) confirmed that the intercellular communication between secretory phosphoprotein 1 (SPP1)-cluster of differentiation (CD44), insulin-like growth factor (IGF)-1-IGF1r and visfatin-insulin receptor (Insr) associated with bone metabolism and insulin metabolism was increased and enhanced in the liver at 6 w post-infection. Overall, we provide the comprehensive single-cell transcriptome landscape of the liver in mice during the progression of schistosome infection and delineate the key cellular and molecular events involved in schistosome infection-induced liver injury and fibrosis. …”
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Effects of Dietary β-Carotene on the Gonadal Color, Pigmentation, and Regulation Mechanisms in Sea Urchin Strongylocentrotus Intermedius by Weixiao Di, Yinuo Zhang, Huinan Zuo, Haijing Liu, Lina Wang, Jun Ding, Yaqing Chang, Rantao Zuo

“…This study aims to clarify the dose–response relationship between dietary β-carotene levels and gonadal pigment deposition and regulation mechanisms related to the carotenoid synthesis of <i>Strongylocentrotus intermedius</i> based on a 60-day feeding trial and subsequent transcriptome analysis. Adult sea urchins (initial weight: 9.33 ± 0.21 g) of three cages were given one of the dry feeds with different doses of β-carotene (0 mg/kg, 150 mg/kg, 300 mg/kg) or fresh kelp (<i>Saccharina japonica</i>). …”
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Entrectinib can induce nerve cell damage by inhibiting PI3K-AKT and TGF-β signaling pathways by Qingshan Tang, Jiachen Dong, Feng Zhang, Dan Zhao, Qi Yang, Jiayu Wen, Yuhao Sun, Jifu Wei, Zhixian Liu

“…Cell apoptosis was measured by flow cytometry. Next, transcriptome sequencing technology was performed to identify differentially expressed genes (DEGs). …”
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Usp18 Mediates D-Dopachrome Tautomerase-Induced Astrocytic Inflammation After Spinal Cord Injury by Zhang X, Hou Y, Cai R, Zhou Y, He B, Cao Z, Li A, Song H, Wang Y, Jiang H, Qi L, Wang Y

“…Primary astrocytes were treated by different concentration of D-DT, either for transcriptome sequencing or for analysis of D-DT-mediated expression of Usp18. …”
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Genome-Wide Analysis of the <i>CDPK</i> Gene Family in <i>Populus tomentosa</i> and Their Expressions in Response to Arsenic Stress and Arbuscular Mycorrhizal Fungi Colonization by Minggui Gong, Jiajie Su, Shuaihui Wang, Youjia Wang, Weipeng Wang, Xuedong Chen, Qiaoming Zhang

“…The analysis of genes provided insights into the evolutionary dynamics and expansion of the <i>PtCDPK</i> gene family within <i>P. tomentosa</i>. …”
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Transcriptional and Genomic Targets of Neural Stem Cells for Functional Recovery after Hemorrhagic Stroke by Le Zhang, Wenjing Tao, Hua Feng, Yujie Chen

“…Recently, emerging evidence from the use of new technologies such as next-generation sequencing and transcriptome profiling has provided insight into our understanding of genomic function and regulation of NSCs. …”
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GAN-WGCNA: Calculating gene modules to identify key intermediate regulators in cocaine addiction. by Taehyeong Kim, Kyoungmin Lee, Mookyung Cheon, Wookyung Yu

“…GAN-WGCNA enables correlation calculations between phenotype and gene expression profiles and visualizes time-series gene module interplay. We analyzed a transcriptome dataset of two weeks of cocaine self-administration in C57BL/6J mice. …”
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In vitro generation of neuromesodermal progenitors reveals distinct roles for wnt signalling in the specification of spinal cord and paraxial mesoderm identity. by Mina Gouti, Anestis Tsakiridis, Filip J Wymeersch, Yali Huang, Jens Kleinjung, Valerie Wilson, James Briscoe

“…Systematic analysis of the transcriptome during differentiation identifies the molecular correlates of each of the cell identities and the routes by which they are obtained. …”
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Integrated miRNA–mRNA Profiling of C2C12 Myoblasts Indicates Regulatory Interactions Involved in Proliferation and Differentiation by Xiaolong Chang, Junwu Ma

“…In addition, we found that genes such as <i>IGF1</i> and <i>Dio2</i> were continuously upregulated during differentiation, and IGF1 might be regulated by multiple miRNAs during this process. This study provides key molecular insights for a deeper understanding of muscle development and regeneration.…”
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Light-mediated activation of PpPSY enhances β-carotene accumulation in pear fruit peel by Li Zhang, Wei Du, Junfan Tu, Hongyan Zhu, Xianming Li

“…In conclusion, the AGL8-LFY complex coactivates PSY expression, regulating β-carotene accumulation in pear fruit. This study provides new insights into the regulatory network governing fruit peel coloration, with potential applications for cultivation strategies to improve fruit quality.…”
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Comprehensive analysis of lipid metabolic signatures identified CEBPD promotes breast cancer cell proliferation by Yu Zhao, Huan He, Linyan Huang, Linna Yu

“…In this study, we leveraged scRNA-seq and bulk transcriptome data to assess the expression patterns and prognostic significance of lipid metabolism-related genes in BRCA. …”
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Host glycan sugar-specific pathways in Streptococcus pneumoniae: galactose as a key sugar in colonisation and infection [corrected]. by Laura Paixão, Joana Oliveira, André Veríssimo, Susana Vinga, Eva C Lourenço, M Rita Ventura, Morten Kjos, Jan-Willem Veening, Vitor E Fernandes, Peter W Andrew, Hasan Yesilkaya, Ana Rute Neves

“…By measuring intracellular metabolites, enzymatic activities and mutant analysis, we provide an accurate map of the biochemical pathways for galactose, mannose and N-acetylglucosamine catabolism in S. pneumoniae. …”
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Global and gene-specific translational regulation in Escherichia coli across different conditions. by Di Zhang, Sophia Hsin-Jung Li, Christopher G King, Ned S Wingreen, Zemer Gitai, Zhiyuan Li

“…Here, we quantified genome-wide transcriptome and relative translation efficiency (RTE) under 12 different conditions in Escherichia coli. …”
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Identification of stable reference genes for qRT-PCR in Stropharia rugosoannulata using mRNA-sequencing data. by Xiaohua Zhang, Xuesong Li, Rong Hua, Yuan Fang, Tingsong Yue, Jianying Li, Yuxun Lu, Wansong Yue, Zhanghui Gao, Shaoxiong Liu, Dafeng Sun

“…In conclusion, Our findings provide robust guidelines for selecting suitable reference genes, thereby enhancing the reliability of qRT-PCR normalization in Stropharia rugosoannulata.…”
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Mycoviruses: trends in plant-fungus-mycovirus interactions and ‘biocontrol’ prospects in agriculture and the environment by Elias Mjaika NDIFON, Gilbert Nchongboh CHOFONG

“…There is a scarcity of information about them, which necessitated this review to provide some leads on where research should focus. …”
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Phosphoproteome dynamics of Saccharomyces cerevisiae under heat shock and cold stress by Evgeny Kanshin, Peter Kubiniok, Yogitha Thattikota, Damien D'Amours, Pierre Thibault

“…Responses to elevated temperatures have been studied in yeast and other model organisms using transcriptome profiling and provided valuable biological insights on molecular mechanisms involved in stress tolerance and adaptation to adverse environment. …”
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