Transcriptomic Analysis of the Negative Effect of Epigallocatechin-3-Gallate from Tea Plant (<i>Camellia sinensis</i>) on <i>Agrobacterium</i>-Mediated Transformation Efficiency by Guizhi Liu, Na Tian, Lan Chen, Siyi Xie, Jinyu Hu, Qifang Jin, Chenyu Shao, Mengdi Huang, Qin Su, Jianan Huang, Zhonghua Liu, Shuoqian Liu

“…These results elucidate the dynamic mechanisms by which EGCG affects <i>Agrobacterium</i> at both the physicochemical and molecular levels, providing a theoretical basis for optimizing genetic transformation in tea plants.…”
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Transcriptomic analysis of Myxococcus xanthus csgA, fruA, and mrpC mutants reveals extensive and diverse roles of key regulators in the multicellular developmental process by Mark A. Farrugia, Ramya Rajagopalan, Lee Kroos

“…Conclusions By comparing wild-type and mutant transcriptomes midway in development, this study documents individual and coordinate regulation of crucial pathways by CsgA, FruA, and MrpC, providing a valuable resource for future investigations.…”
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Applying integrated transcriptome and single-cell sequencing analysis to develop a prognostic signature based on M2-like tumor-associated macrophages for breast cancer by Yanghaochen Xu, Peiyan Lin, Ye Zhu, Qing Zhang, Jinhong Zhou

“…Conclusion We identified 10 M2-like TAM-related prognostic signature genes for BRCA, providing potential therapeutic targets for the treatment of the cancer.…”
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Prospects for using high-throughput sequencing methods to identify new biomarkers of response and resistance to antitumor therapy by M. А. Sorokina, T. R. Grishina

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Sevoflurane exposure in early life: mitochondrial dysfunction and neurotoxicity in immature rat brains without long-term memory loss by Lin Qiu, Hongwei Li, Bingbing Li, Joakim Ek, Xiaoli Zhang, Yiwen Chen, Zehua Shao, Jie Zhang, Jiaqiang Zhang, Hongqi Lin, Changlian Zhu, Yiran Xu, Xiaoyang Wang

“…Metabolomics analysis revealed significant changes in fatty acid and mitochondrial energy metabolism. Transcriptomic analysis identified altered gene expression related to neurodevelopment and mitochondrial function. …”
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CHST3, PGBD5, and SLIT2 can be identified as potential genes for the diagnosis and treatment of osteoporosis and sarcopenia by Xingyao Yang, Zhangzhen Du, Shuxing Xing

“…This study aims to use transcriptomics and explore common diagnostic genes of osteoporosis and sarcopenia and predict potentially effective treatment drugs. …”
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Novel single-cell preservation and RNA sequencing technology unlocks field studies for Plasmodium natural infections by Erin Sauve, Pieter Monsieurs, Pieter Guetens, Roberto Rudge de Moraes Barros, Anna Rosanas-Urgell

“…When applied to unicellular eukaryotes such as Plasmodium, scRNA-seq provides a single-cell resolution valuable to study complex infections comprised of mixed lifecycle stages and clones. …”
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The proteotranscriptomic characterization of venom in the white seafan Eunicella singularis elucidates the evolution of Octocorallia arsenal by Maria Vittoria Modica, Serena Leone, Marco Gerdol, Samuele Greco, Didier Aurelle, Marco Oliverio, Giulia Fassio, Khadija El Koulali, Célia Barrachina, Sebastien Dutertre

“…To fill this gap, we applied a proteo-transcriptomic approach to investigate venom composition in Eunicella singularis, a gorgonian species common in Mediterranean hard-bottom benthic communities. …”
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An Integrated Analysis of Transcriptomic and Metabolomic Effects Reveals Insights into Stress Responses in Largemouth Bass (<i>Micropterus salmoides</i>) Under MS-222 (Tricaine Met... by Ping Gao, Rimeng Chen, Deyun Ma, Shanshan Lin, Haodong Yu, Xuezhen Zhang

“…Therefore, this study investigated the tissue-specific transcriptomic and metabolomic effects of MS-222 anesthesia on largemouth bass (<i>Micropterus salmoides</i>). …”
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Nitroxoline evidence amoebicidal activity against Acanthamoeba castellanii through DNA damage and the stress response pathways by Lijun Chen, Wei Han, Wenwen Jing, Meng Feng, Qingtong Zhou, Xunjia Cheng

“…In this study, nitroxoline significantly reduced the viability of A. castellanii trophozoites in a dose- and time-dependent manner, inducing morphological changes and apoptosis. Transcriptomic analysis revealed substantial alterations in gene expression, including enrichment of metabolic pathways, DNA damage responses, and iron ion binding. …”
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The Effects of FR and UVA Irradiation Timing on Multi-Omics of Purple Lettuce in Plant Factories by Yubin Zhang, Zhaoxin Li, Ning Zhang, Xiujuan Chai

“…Metabolomic analysis corroborated the transcriptomic findings, with particular emphasis on antioxidant activity, photoprotection, and defense mechanisms. …”
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Proteogenomic characterization of highly enriched viable leukemic blasts in acute myeloid leukemia: A SWOG report by Jasmine Naru, Megan Othus, ChenWei Lin, Melinda A. Biernacki, Marie Bleakley, Thomas R. Chauncey, Harry P. Erba, Min Fang, Matthew P. Fitzgibbon, Phillip R. Gafken, Richard G. Ivey, Jacob J. Kennedy, Travis D. Lorentzen, Soheil Meshinchi, Anna Moseley, Era L. Pogosova‐Agadjanyan, Vivian M. Liu, Jerald P. Radich, Uliana J. Voytovich, Pei Wang, Jeffrey R. Whiteaker, Cheryl L. Willman, Feinan Wu, Amanda G. Paulovich, Derek L. Stirewalt

“…Conclusion Together, the results provide insight into the biology of VLBs and demonstrate the gains derived from examining the proteome in addition to genome and transcriptome.…”
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In silico analysis of hub genes and regulatory networks implicates the putamen in non-motor Parkinson’s disease disorders by Stephen Tunmise Akanbi, Joshua Ayodele Yusuf, Thompson Oluwaferanmi Ayandele, Dayo Samson Oladipupo, Darasimi Racheal Olorunlowu, Blessing Dorcas Olawuyi, Joshua Oluwafisayo Adepoju, Dolapo Emmanuel Opasina, Elizabeth Kehinde Opoola, Uchenna Victor Ugwuanyi, Olufunto Omodele Adeleye

“…This study aims to identify the role of putamen in non-motor PD symptoms as well as potential therapeutic target in the putamen of PD. Methods Transcriptome profiles of PD (dataset number: GSE205450, obtained from postmortem putamen and caudate samples from forty controls and thirty-five PD patients) were retrieved from the Gene Expression Omnibus (GEO) database. …”
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Integrating spatial and single-cell transcriptomes reveals the role of COL1A2(+) MMP1(+/-) cancer-associated fibroblasts in ER-positive breast cancer by Zhi-Hao Yu, Huan-Ling Xu, Shuo Wang, Ying-Xi Li, Gui-Xin Wang, Yao Tian, Zhao-Hui Chen, Wen-Bin Song, Long He, Xin Wang, Xu-Chen Cao, Yue Yu

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Impact on the Leishmania mexicana transcriptome due to knockout of genes encoding orthologs of methyltransferases involved in m1A and m5C mRNA modifications by Angela Moreira Bezerra, Ariely Barbosa Leite, Christian Robson de Souza Reis, João Luiz de Lemos Padilha Pitta, Suellen Rodrigues Maran, Nilmar Silvio Moretti, Danielle Maria Nascimento Moura, Antonio Mauro Rezende

“…Conclusions Our findings provide insights into the role of these methyltransferases orthologs in the regulation of trypanosomatid transcriptome, contributing to our understanding of gene expression control in this parasite. …”
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Transcriptomic Analysis of Differentially Expressed Genes during Flower Organ Development in Genetic Male Sterile and Male Fertile Tagetes erecta by Digital Gene-Expression Profili... by Ye Ai, Qinghua Zhang, Weining Wang, Chunling Zhang, Zhe Cao, Manzhu Bao, Yanhong He

“…This is the first transcriptome analysis in T. erecta and will provide a valuable resource for future genomic studies, especially in flower organ development and/or differentiation.…”
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Comparative Analyses of IGF-Induced Liver Transcriptomes Reveal Genes and Signaling Pathways Associated with Ovarian Growth and Development in Golden Pompano (<i>Trachinotus ovatus... by Yan Wang, Charles Brighton Ndandala, Muhammad Fachri, Vicent Michael Shija, Pengfei Li, Huapu Chen

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Transcriptome-based protein-protein interaction analysis reveals immune gene network elucidating white body immunity mechanisms in response to LPS stimulation in Amphioctopus fangs... by Zhengcai Lu, Yancheng Zhao, Tingjin Lv, Xipan Chen, Cuiju Cui, Xiumei Liu, Zan Li, Liyong Wang, Xiaohui Xu, Jianmin Yang

“…In the present research, transcriptome sequencing and bioinformatics analysis were conducted on A. fangsiao white body tissue after 6 h and 24 h of LPS stimulation. …”
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Trophoblast cell response to periodontal pathogens unveils oxidative stress networks between periodontitis and pre-eclampsia: Mendelian randomization, transcriptomic analysis, and... by Lihua Hu, Shuqin Liu

“…Methods We employed a multi-faceted approach combining Mendelian Randomization (MR) analysis, transcriptomic data mining, and in vitro experiments. …”
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Mesquite seed flour as a nutrient-rich alternative to fishmeal for common carp fingerlings (Cyprinus carpio): Environmental, growth performance, transcriptomic and intestinal micro... by María Fernanda Barragán-Longoria, Karla Jareth Pérez-Viveros, Arturo Cadena-Ramírez, Javier Castro-Rosas, José Roberto Villagómez-Ibarra, Jesus Hernandez-Perez, Silvia Hinojosa-Alvarez, Carlos Alberto Gómez-Aldapa, Rocio Alejandra Chavez-Santoscoy

“…Both MD and FM diets provided optimal water quality conditions for the growth and well-being of fish during the experiment. …”
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