Investigation of the impact of ultraviolet B irradiation on apoptosis and proliferation in A375 melanoma cells by Wang Jingyang, Yuan Zhixiang, Chen Taoyu, Guo Jiaqi, Qu Ying, Hou Tao, Zhu Lvyun, Shao Tong

“…Transcriptomic analysis identified 303 differentially expressed genes, with p53 signaling emerging as the central regulator. …”
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FAM111B knockdown attenuates tumorigenesis of ovarian cancer via the downregulation of MYC by Guoyu Yu, Fang Wei, Wanying Li, Qiuyun Guo, Lihong Zhang

“…Additionally, protein transcriptomic analysis implicated FAM111B in genetic-information processing via the MYC pathway, underscoring FAM111B’s central role in ovarian cancer tumorigenesis. …”
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Multi-omics profiling of Nanhaia speciosa and Nanhaia fordii: insights into lectin dynamics, nodulation, and triterpenoid saponin biosynthesis by Zhiying Li, Jiabin Wang, Junfang Zhang, Yunliu Fu, Yonglin Jing, Bilan Huang, Huazhou Wu, Chunyang Meng, Li Xu

“…Moreover, the nodulation key gene RPG cannot be expressed in the roots of N. speciosa, possibly explaining the ability of N. fordii to form nodules while N. speciosa cannot. Conclusions Leveraging high-quality haploid genome assembly and multi-omics analysis, our data provides a crucial foundation for identifying key metabolic components and candidate genes associated with important traits and for breeding new varieties of N. fordii and N. speciosa.…”
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Identification of macrophage-associated diagnostic biomarkers and molecular subtypes in gestational diabetes mellitus based on machine learning by Kai Wei, Liyun Yuan, Yongsheng Ge, Han Yu, Guoping Zhao, Guoqing Zhang, Guohua Liu

“…For scRNA-seq data, cell clusters were annotated using the SingleR package and validated with marker gene expression profiles, while hdWGCNA analysis identified three gene modules related to macrophages. …”
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Microglial TLR4-Lyn kinase is a critical regulator of neuroinflammation, Aβ phagocytosis, neuronal damage, and cell survival in Alzheimer’s disease by Rezwanul Islam, Hadi Hasan Choudhary, Feng Zhang, Hritik Mehta, Jun Yoshida, Ajith J. Thomas, Khalid Hanafy

“…The DAM population in 5XFAD mice which produce more inflammatory cytokines and phagocytose more Aβ were observed to express greater levels of TLR4 and Lyn. Pathway analysis comparison between WT, 5XFAD, and 5XFAD x Lyn-/- mice supported these findings via our microglial spatial transcriptomic analysis. …”
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Enhance the therapeutic efficacy of human umbilical cord-derived mesenchymal stem cells in prevention of acute graft-versus-host disease through CRISPLD2 modulation by Qing Xu, Rui Wang, Ke Sui, Yuxi Xu, Ya Zhou, Yuxuan He, Ziyi Hu, Qi Wang, Xiaodong Xie, Xiaoqi Wang, Shijie Yang, Lingyu Zeng, Jiang F. Zhong, Zheng Wang, Qingxiao Song, Xi Zhang

“…Methods To investigate MSCs heterogeneity, we conducted single-cell transcriptomic analysis of human umbilical cord-derived MSCs (HUC-MSCs) and identified key feature genes that distinguish MSCs subpopulations. …”
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Endurance training promotes chromatin closure and timely repression of the post-exercise immediate early stress response by Laura M. de Smalen, Volkan Adak, Aurel B. Leuchtmann, Konstantin Schneider-Heieck, Stefan A. Steurer, Christoph Handschin

“…Gene expression was assessed via RNA-sequencing, and motif activity analysis identified regulatory factors involved in exercise-induced chromatin remodeling and transcriptomic response. …”
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A multi-type programmed cell death gene signature predicts survival and reveals therapeutic targets in osteosarcoma by Chunyang Wu

“…Lysosome-dependent cell death, apoptosis and anoikis emerged as key PCD pathways in OS. Single-cell analysis revealed COL13A1 expression in malignant cells while GM2A and FUCA1 were enriched in macrophages. …”
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Behçet syndrome: The disturbed balance between anti‐ (CLEC12A, CLC) and proinflammatory (IFI27) gene expressions by Ali Kemal Oğuz, Çağdaş Şahap Oygür, Seda Taşır, Hilal Özdağ, Mehmet Nejat Akar

“…A microarray‐based comparative transcriptomic analysis was performed to elucidate the molecular mechanisms of BS and identify any potential therapeutic targets. …”
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HERV-derived epitopes represent new targets for T-cell-based immunotherapies in ovarian cancer by Qing Wang, Maha Ayyoub, Olivia Le Saux, Paola Bonaventura, Isabelle Treilleux, Nicolas Chopin, Clarisse Dubois, Virginie Mutez, Nicolas Chuvin, Yann Estornes, Jenny Valladeau-Guilemond, Stephane Depil, Nicolas Gadot, Marie Michelas, Audrey Page, Olivier Tabone, Marie Delles, Sarah Moran, Thibault Richard, Marjorie Lacourrège, Dina M Tawfik, Ema Etchegaray, Adrian Valente, Rasha E Boulos, Gabriel Jimenez Dominguez

“…Human endogenous retroviruses (HERVs) are aberrantly expressed by tumor cells and may represent a source of shared T-cell epitopes for cancer immunotherapy regardless of the tumor mutational burden.Methods A transcriptomic analysis based on RNA sequencing was developed to quantify the expression of HERV-K sequences containing the selected epitopes. …”
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Ability of SPP1 to Alleviate Post‐Intracerebral Hemorrhage Ferroptosis via Nrf2/HO1 Pathway by Pengpeng Li, Zhenxin Tao, Yangyang Gao, Zhengqian Mu, Jiajia Tian, YaTing Zhang, Wenhui Yang, Yilu Li, Xudong Zhao

“…ABSTRACT Purpose This study aimed to investigate the role of secretory phosphoprotein 1 (SPP1/OPN) in modulating iron‐induced cell death (ferroptosis) following intracerebral hemorrhage (ICH). By integrating transcriptomic analysis and experimental validation, we sought to identify key molecular pathways and therapeutic targets associated with ferroptosis in ICH. …”
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Endophytic fungi enhance drought tolerance in Fagopyrum tataricum: Insights into flavonoid biosynthesis and photosynthetic pathways by Yujie Jia, Qiqi Xie, Jiwen Tao, Yixin Chen, Yixuan Qi, Hongying Zhu, Tongliang Bu, Xinyu Zhang, Yirong Xiao, Zhao Chen, Qingfeng Li, Zizhong Tang, Ming Yuan

“…J46 and J79 increased flavonoid content in the leaves of F. tataricum by 28.39 % and 19.54 %, respectively, and in the seeds by 17.79 % and 14.06 %, respectively. Metabolite analysis revealed elevated levels of osmotic regulatory substances and antioxidants, while photosynthetic inhibition caused by drought stress was effectively alleviated upon fungal inoculation. …”
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Delayed Starch Degradation Triggers Chromoplast Structural Aberration to Inhibit Carotenoid Cleavage: A Novel Mechanism for Flower Color Deepening in <i>Osmanthus fragrans</i> by Xiangling Zeng, Yunfei Tan, Xin Wen, Qiang He, Hui Wu, Jingjing Zou, Jie Yang, Xuan Cai, Hongguo Chen

“…Transcriptomic analysis indicates that carotenoid metabolic pathway genes do not correlate directly with the phenotype; however, 49 candidate genes significantly associated with pigment accumulation were identified. …”
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Re-evaluating evidence for giant genomes in amoebae by Daniel Barzilay, João P. B. Alcino, Giulia M. Ribeiro, Alfredo L. P. Sousa, Daniel J. G. Lahr

“…Fully sequenced amoebozoa genomes range from 14.4 to 52.37 mega basepairs, well within the typical single-celled eukaryote expectation. While the whole genome of the historically relevant Amoeba proteus has not yet been fully sequenced, we provide here a statistical analysis using protein-coding genes from transcriptomic data, suggesting that the genome size is consistent with this range, far smaller than previously claimed. …”
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CD300f epitopes are specific targets for acute myeloid leukemia with monocytic differentiation by Edward Abadir, Robin E. Gasiorowski, Kaitao Lai, Fiona Kupresanin, Adelina Romano, Pablo A. Silveira, Tsun‐Ho Lo, Phillip D. Fromm, Marina L. Kennerson, Harry J. Iland, P. Joy Ho, P. Mark Hogarth, Kenneth Bradstock, Derek N.J. Hart, Georgina J. Clark

“…To confirm the value of CD300f as a leukemic target, we showed that CD300f antibodies bind to AML from 85% of patient samples. While one CD300f monoclonal antibody (mAb) reportedly did not bind healthy hematopoietic stem cells, transcriptomic analysis found that CD300f transcripts are expressed by healthy HSPC. …”
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PARP9-PARP13-PARP14 axis tunes colorectal cancer response to radiotherapy by Rimvile Prokarenkaite, Karolina Kuodyte, Greta Gudoityte, Elzbieta Budginaite, Daniel Naumovas, Egle Strainiene, Kristijonas Velickevicius, Audrius Dulskas, Ernestas Sileika, Jonas Venius, Virginijus Tunaitis, Augustas Pivoriunas, Vytaute Starkuviene, Vaidotas Stankevicius, Kestutis Suziedelis

“…Gene set enrichment analysis was conducted to determine the pathways in which PARP13 is engaged. …”
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Identification and characterization of seminal fluid proteins in the Asian tiger mosquito, Aedes albopictus. by Kathryn E Boes, José M C Ribeiro, Alex Wong, Laura C Harrington, Mariana F Wolfner, Laura K Sirot

“…Despite the importance of Sfps on female reproductive behavior in mosquitoes and other insects, the identity of Sfps in Ae. albopictus has not previously been reported. We used transcriptomics and proteomics to identify 198 Sfps in Ae. albopictus. …”
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Effect of dietary replacement of fish meal by poultry by-product meal on the growth and hepatic health in loach (Paramisgurnus dabryanus) by Yongan Li, Chuanqi Yu, Shuyao Li, Youjie Li, Zhiwen Yuan, Jie Pan, Qi Chen, Yaping Li, Qiubai Zhou, Zirui Wang

“…Moreover, primary bile acid biosynthesis was the only one pathway enriched in top 20 significant pathways by transcriptomic and metabolomic analysis. Specifically, the key bile acid synthesis gene CYP7a1 was down-regulated, while CYP7b1 evinced an up-regulated pattern in PBM50 group compared to PBM0 group. …”
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Establishment of a Novel in vitro Model of Sepsis-Induced Myocardial Injury Using Septic Serum: A Comprehensive Comparative Study by Yang H, Feng L, Jiang Z, Deng R, Wu X, Zeng K

“…The mRNA expression profiles were analyzed to identify differentially expressed genes (DEGs), followed by functional enrichment analysis. The diagnostic utility of each model was assessed using receiver operating characteristic (ROC) analysis.Results: While LPS and TNF-α-treated cardiomyocytes exhibited similar injury features, both only partially captured the complexity of the sepsis-induced myocardial injury phenotype. …”
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Medical Hemorrhoid Gel Ameliorates Croton Oil-Induced Hemorrhoids by Suppressing the NLRP3 Inflammasome Activation via NF-&amp;kappa;B Signaling Pathway by Ai Z, Yuan D, Li Y, Cai J, Zhou D, Liu W

“…Acute toxicity tests showed that MHG did not cause anorectal abnormalities or systemic toxicity in rats. Transcriptomic analysis integrated with experimental validation suggested the therapeutic mechanism of MHG involves inflammation response and NF-κB pathway. …”
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