The induction effect of hydroxyurea and metformin on fetal globin in the K562 cell line by Mohammad Eini, Hossain Safarpour, Ebrahim Miri-Moghddam

“…Understanding these mechanisms is paramount for identifying alternative therapeutic approaches to increase Hb F production while minimizing adverse effects. In this study, we employed weighted gene co-expression network analysis (WGCNA) to investigate the molecular underpinnings of γ-globin switching within GSE90878 dataset. …”
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Multi-omics reveals effects of diet FNDF/starch level on growth performance and rumen development of Hu sheep by Haibi Zhao, Jiqing Wang, Zhiyun Hao, Pengfei Yin, Shanglong Wang, Yanli Guo, Chunyan Ren

“…Rumen epithelial transcriptome sequencing analysis identified 825 (A vs. …”
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Automation of RNA-Seq Sample Preparation and Miniaturized Parallel Bioreactors Enable High-Throughput Differential Gene Expression Studies by Karlis Blums, Josha Herzog, Jonathan Costa, Lara Quirico, Jonas Turber, Dirk Weuster-Botz

“…To gain a molecular understanding of the microbial production strains in miniaturized parallel single-use bioreactors, we extended the at-line monitoring procedures to transcriptome analysis in a parallel approach using RNA-Seq. …”
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Role of integrin α4 in the inhibition of fibrosis in activated hepatic stellate cells by Periplaneta americana extract by Ying Fang, Ye Liu, Dingchun Li, Yi Miu, Kexuan Chen, Jv Zhou, Lijuan Xie, Xinting Chen, Jingyan Wu, Ying Zhu, Lechun Lv, Wu Li

“…Molecular mechanisms were investigated through western blot (WB), quantitative PCR (QPCR), and transcriptome analysis. Results indicate that PAE reduces hepatic fibrosis by curbing hepatic stellate cells (HSCs) proliferation, migration, collagen synthesis, inflammatory cytokine production, and epithelial-mesenchymal transition (EMT). …”
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A gene expression atlas of Nicotiana tabacum across various tissues at transcript resolution by Shizhou Yu, Jufen Wan, Jufen Wan, Tenghang Xu, Tenghang Xu, Jie Zhang, Linggai Cao, Jie Liu, Hongfeng Liu, Xueliang Ren, Zhixiao Yang

“…In this study, we collected 599 tobacco RNA-seq datasets from 35 projects. 207,689 transcripts were identified in this study, of which 35,519 were annotated in the reference genome, while 172,170 transcripts were newly annotated. Additionally, tissue-specific analysis revealed 4,585 transcripts that were uniquely expressed in different tissues, highlighting the complexity and specialization of tobacco gene expression. …”
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Role of Bifidobacterium animalis subsp. lactis BB-12 in mice with acute pancreatitis by Bingbing Du, Ren Yan, Xiaoxiang Hu, Jing Lou, Yixin Zhu, Yini Shao, Huiyong Jiang, Yingying Hao, Longxian Lv

“…Transcriptome analysis revealed that BB-12 mitigated the AP-induced dysregulation of several pathways, specifically attenuating the upregulation of the pancreatic secretion and ascorbate and aldarate metabolism pathways while reversing the downregulation of the ribosome, oxidative phosphorylation, and thermogenesis pathways. …”
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Effect and mechanism of sodium butyrate on the activation of Epstein-Barr virus in Epstein-Barr virus-positive gastric cancer cells by TIAN Zhaoxin, CHEN Yuying, LIU Wen

“…The GO functional enrichment analysis and the KEGG pathway enrichment analysis were performed for all DEGs identified, and the proteins enriched in significant pathways (the pathways with P<0.05 in the KEGG pathway enrichment analysis) were considered key pathway proteins, while Western blotting was used to mea-sure the relative expression levels of key pathway proteins in groups A, B, and C. …”
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Unveiling the Temporal Dynamics and Molecular Regulation Profiles of Neutrophil Extracellular Traps Following Spinal Cord Injury by Li J, Chang C, Li Y, Cui S, Bai J, Zhang C, Wang X, Li K, Jian F

“…GSVA revealed peak NET score at day 1 post-injury, with attenuation at days 3 and 7. Single-cell transcriptome analysis demonstrated predominant expression of these key genes in neutrophils during the acute phase, most prominently at 1 day post-injury, which coincides with the most pronounced neutrophil infiltration. …”
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Comprehensive Genome-Wide Characterization of L-Type Lectin Receptor-like Kinase (L-LecRLK) Genes in Wheat (<i>Triticum aestivum</i> L.) and Their Response to Abiotic Stress by Wan Zhao, Fuyan Zhang, Jiahuan Wang, Shuai Fang, Zhongjie Cheng, Xuhui Ma, Jialin Fan, Zhaoshi Xu, Xiaojie Chen

“…Gene duplication analysis revealed that both whole-genome/segmental and tandem duplications contributed to family expansion, while Ka/Ks ratio analysis suggested that the genes have undergone strong purifying selection. …”
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Ethyl β-carboline-3-carboxylate targets PRDX5/c-Jun axis for novel therapeutic strategy against cervical cancer by Wan-Qiu Xiao, Dong-Hun Lee, Hakjin Kim, Hui-Na Zhang, Yao-Yuan Feng, Ying-Hua Jin, Mei-Hua Jin, Ying-Hao Han, Taeho Kwon, Hu-Nan Sun

“…Methods Western blot assay were performed to asses the expression of protein levels; The cellular and mitochondrial ROS and mithochondrial membrane potential were observed with fluorescence microscopy; Bioinformatics analysis were used to check the expression levels of PRDX5 and JUN family proteins and prognosis analysis in cervical cancer; Transcriptome analysis was performed to analyse the gene expression levels between mock and shPRDX 5 cells; Serum TNF-α and INF-γ levels were detected by ELISA kits; HE staining analysis were performed to check the organ histopathological changes in mice. …”
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Identification and Validation of Key Genes Involved in the Coupling of Mitochondria-Associated Endoplasmic Reticulum Membrane in Hemorrhoidal Disease by Mao L, Rao Z, Wang Y, Yang J, He J, Zheng Z, Chen L

“…Differential expression analysis and single-sample Gene Set Enrichment Analysis (ssGSEA) scores were initially employed to identify candidate genes. …”
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The combination of polystyrene microplastics and di (2-ethylhexyl) phthalate promotes the conjugative transfer of antibiotic resistance genes between bacteria by Yu Li, Xiaomei Liu, Saisai Guo, Lan Wang, Jingchun Tang

“…This indicated that the effects of DEHP and microplastics on ARGs transfer might be antagonistic. Transcriptome analysis indicated that the transfer of ARGs affects bacterial ion binding, oxidative stress, and energy metabolism processes, while the expression of genes related to cell membrane permeability, DNA repair, bacterial drug resistance, and quorum sensing also increase. …”
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RNF138 contributes to cisplatin resistance in nasopharyngeal carcinoma cells by Hangyu Xu, Qing Yin, Linna Fan, Yating Zhao, Biying Song, Qifan Xu, Jie Zhu, Meifen Xu

“…Moreover, a tumor xenograft mouse model was developed to investigate the role of RNF138 on NPC progression in vivo. Additionally, transcriptome analysis was performed in 5–8 F cells transfection with OE-RNF1138 or OE-NC.Cisplatin significantly inhibited the proliferation, and promoted apoptosis and DNA damage in NPC cells; however, overexpression of RNF138 reversed the aforementioned regulatory role of cisplatin on NPC cells. …”
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Identification of cell adhesion-related subtypes and construction of risk model to predict breast cancer prognostic and immunological properties by De-Ming Lv, Li Yang, Chen Fan, Ling-Hui Fang, Su-Fen Cheng

“…The study aims to identify breast cancer subtypes related to cell adhesion and develop prognostic models that are essential for evaluating the prognostic risk and immunological profile of breast cancer. Methods Transcriptome and clinical data were obtained from The Cancer Genome Atlas (TCGA) database, while cell adhesion-related genes (CARGs) from the MSigDB database. …”
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XMU-MP-1, Inhibitor of STE20-like MST1/2 Kinases of the Hippo Signaling Pathway, Suppresses the Cell Cycle, Activates Apoptosis and Autophagy, and Induces Death of Hematopoietic Tu... by Alexander G. Stepchenko, Sofia G. Georgieva, Elizaveta V. Pankratova

“…Levels of the LC3-II protein were also shown to be increased, while the level of p62 decreased. These changes are associated with apoptosis and autophagy, respectively. …”
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The BES1/BZR1 transcriptional factor SlBES2 regulates photosynthetic apparatus in tomato fruit by Ming Huang, Wenjing Liu, Deding Su, Ghassen Abid, Baowen Huang, Zhengguo Li

“…Comparative transcriptome analysis revealed that multiple genes of the photosystem, chloroplast development and chlorophyll metabolism pathways were regulated by SlBES2. …”
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Long Noncoding RNA–Messenger RNA (lncRNA–mRNA) Network in Resistance to Gummy Stem Blight (<i>Stagonosporopsis cucurbitacearum</i>) of Melon Plant Introduction (PI) 420145 by Rui Zhang, Jing Chen, Yongbing Zhang, Xiumei Lu, Chunyan Cheng, Ji Li, Qunfeng Lou, Yuhui Wang, Chuntao Qian

“…Our results revealed that PI 420145 exhibits a thicker waxy layer on the leaf surface and limited conidial germination without obvious signs of cell damage compared to ‘Baipicui’. The transcriptomic analysis identified a total of 23,078 differentially expressed genes (DEGs) and 974 differentially expressed long noncoding RNAs (DELs). …”
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Functional roles of folic acid in alleviating dexamethasone‐induced fatty liver syndrome in laying hens by Xi Sun, Junjie Ma, Chaohui Wang, Zhouzheng Ren, Xin Yang, Xiaojun Yang, Yanli Liu

“…FA significantly reversed hepatic lipid deposition, and 57 differentially expressed genes affected by FA were identified in the transcriptome analysis. Their transcriptional and translational levels indicate that in the early FLS, insulin‐like growth factor 2/phosphatidylinositol‐3‐kinase/protein kinase B pathway related to lipid metabolism was activated; folate cycling was inhibited, while endoplasmic reticulum (ER) stress and apoptosis‐related protein abundance were elevated. …”
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Proteomic landscape of Alzheimer’s disease: emerging technologies, advances and insights (2021 – 2025) by Jay M. Yarbro, Him K. Shrestha, Zhen Wang, Xue Zhang, Masihuz Zaman, Mengqi Chu, Xusheng Wang, Gang Yu, Junmin Peng

“…Discrepancies between proteome and transcriptome suggest altered protein turnover in AD. …”
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Assessing Bias and Reproducibility of Viral Metagenomics Methods for the Combined Detection of Faecal RNA and DNA Viruses by Rik Haagmans, Oliver J. Charity, Dave Baker, Andrea Telatin, George M. Savva, Evelien M. Adriaenssens, Penny P. Powell, Simon R. Carding

“…Whole transcriptome amplification (WTA2) and sequence-independent single primer amplification (SISPA) are two widely used methods for combined metagenomic sequencing of RNA and DNA viruses. …”
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