Physiological and transcriptomic analyses reveal the regulatory mechanisms for the adaptation of Quercus robur to shade conditions by Xiong Huang, Qiuhong Hu, Mengke Dou, Cai Liu, Jiangtao Fan, Jia Liu, Peng Zhu

“…In contrast, CHL-a, CHL-b, Car content, SP content, and POD activity exhibited an increasing trend. Transcriptome sequencing was performed on Q. robur samples subjected to different shade treatments: no shade (T1), 40% shade (T3), and 80% shade (T5). …”
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Comprehensive genomic and transcriptomic profiling of pulmonary nodules in synchronous multiple primary lung cancer by Xingsheng Liu, Kun Qian, Lei Su, Xiaoru Tian, Xin Zhao, Tengteng Wang, Li Han, Zhenzhen Li, Peilong Zhang, Ruotian Wang, Baodong Liu, Yuanbo Li, Xiaogang Tan, Yi Zhang

“…Methods We performed targeted DNA sequencing on tumor specimens and conducted bulk RNA transcriptome analysis on 53 multiple nodules originating from 26 lung cancer patients. …”
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Metabolism and immune responses of striped hamsters to ectoparasite challenges: insights from transcriptomic analysis by Xinchang Lun, Yiguan Wang, Ning Zhao, Yujuan Yue, Fengxia Meng, Qiyong Liu, Xiuping Song, Ying Liang, Liang Lu

“…Hosts adjust their physiological and immune states to optimize survival strategies during different ectoparasite stages, enhancing our understanding of host-ectoparasite interactions. …”
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Proteome-wide association studies for blood lipids and comparison with transcriptome-wide association studies by Daiwei Zhang, Boran Gao, Qidi Feng, Ani Manichaikul, Gina M. Peloso, Russell P. Tracy, Peter Durda, Kent D. Taylor, Yongmei Liu, W. Craig Johnson, Stacey Gabriel, Namrata Gupta, Joshua D. Smith, Francois Aguet, Kristin G. Ardlie, Thomas W. Blackwell, Robert E. Gerszten, Stephen S. Rich, Jerome I. Rotter, Laura J. Scott, Xiang Zhou, Seunggeun Lee

“…We found that although PWASs and TWASs can show different directions of associations in an individual gene, 40 out of 49 tissues showed a positive correlation between PWAS and TWAS signed p values across all the genes, which suggests high-level consistency between proteome-lipid associations and transcriptome-lipid associations.…”
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Genomic and Transcriptomic Profiles in Smokers and Never-Smokers Lung Squamous Cell Carcinoma Patients by Canale M, Virga A, Angeli D, Fonzi E, Gnetti L, Dubini A, Tedaldi G, Urbini M, Bocchialini G, Petracci E, Verlicchi A, Cravero P, Citarella F, Bennati C, Andrikou K, Delmonte A, Crinò L, Carbognani P, Ulivi P, Ampollini L

“…Unsupervised hierarchical clustering on transcriptomes effectively identified different specific transcriptional subtypes between smokers and never-smokers. …”
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Comparative analysis of two stored sweet potato varieties using integrated transcriptomics and metabolomics by Xinyi Feng, Jinhua Zuo, Yunxiang Wang, Chunmei Bai, Shaoqing Chen, Lili Ma, Xuelian He, Jiejie Tao, Shiyu Liu, Yiting Ren, Demei Meng, Yanyan Zheng

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Molecular Clustering of Metabolic Dysfunction-Associated Steatotic Liver Disease Based on Transcriptome Analysis by Gina Ryu, Eileen Laurel Yoon, Wankyu Kim, Dae Won Jun

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Blood collection tube and RNA purification method recommendations for extracellular RNA transcriptome profiling by The exRNAQC Consortium

“…In addition, we assessed interactions among a selected pre-analytical variable set, resulting in 456 extracellular transcriptomes. Blood preservation tubes failed to stabilize exRNA and RNA purification methods differed significantly in performance, causing variations in concentration, detected gene numbers, replicability and observed transcriptome complexity. …”
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Skin transcriptomics of invasive Coqui frogs: stress responses, parasite signatures, and antimicrobial peptides. by Randy Ortiz, Leeann C Dabydeen, Carolyn Kosinski, Priyanka Gera, Juan D Carvajal-Castro, Victoria Akilov, Hunter J Howell, Emily Powell, Juan C Santos

“…Our results show differences in stress response gene signatures between both populations. …”
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The Acrasis kona genome and developmental transcriptomes reveal deep origins of eukaryotic multicellular pathways by Sanea Sheikh, Cheng-Jie Fu, Matthew W. Brown, Sandra L. Baldauf

“…Here, we report the Acrasis kona genome sequence plus transcriptomes from pre-, mid- and post-developmental stages. …”
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Non-human primate seasonal transcriptome atlas reveals seasonal changes in physiology and diseases by Junfeng Chen, Kousuke Okimura, Liang Ren, Yusuke Nakane, Tomoya Nakayama, Yang Chen, Kai Fukawa, Soutarou Sugiyama, Takayoshi Natsume, Naoko Suda-Hashimoto, Mayumi Morimoto, Takako Miyabe-Nishiwaki, Takao Oishi, Yuma Katada, Manhui Zhang, Kohei Kobayashi, Shoko Matsumoto, Taiki Yamaguchi, Ying-Jey Guh, Issey Takahashi, Taeko Nishiwaki-Ohkawa, Daiki X. Sato, Yoshiharu Murata, Kenta Sumiyama, Atsushi J. Nagano, Hiroo Imai, Takashi Yoshimura

“…We find seasonal changes in plasma metabolites and hormones. Transcriptome analysis identifies sex differences in seasonally oscillating genes (SOGs) in all tissues studied, and we generate the web database ‘Non-Human Primate Seasonal Transcriptome Atlas (NHPSTA).’ …”
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Blood Transcriptome Profiling Highlights the Role of Intestinal Bacterial Translocation in Severe COVID-19 by Dimitrios Christos Tremoulis, Gethsimani Papadopoulou, Vasiliki Pogka, Aikaterini Argyraki, Giota Lourida, Andreas Mentis, Timokratis Karamitros

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Transcriptomics-informed pharmacology identifies epigenetic and cell cycle regulators that enhance AAV production by Joshua Tworig, Francis Grafton, Kaylin Fisher, Markus Hörer, Christopher A. Reid, Mohammad A. Mandegar

“…In this study, we aimed to identify targets that may enhance rAAV production using transcriptomic analyses of five cell lines with variable capacities for rAAV production. …”
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BRAFV600E‐PROTAC versus inhibitors in melanoma cells: Deep transcriptomic characterization by Solomon O. Alhassan, Zakaria Y. Abd Elmageed, Youssef Errami, Guangdi Wang, Joe A. Abi‐Rached, Emad Kandil, Mourad Zerfaoui

“…Although PROTAC and inhibitor treatments caused overlapping transcriptomic changes, key differences were observed. …”
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Dermal fibroblast transcriptome indicates contribution of WNT signaling pathways in the pathogenesis of Apert syndrome by Arda Çetinkaya, Ekim Taşkıran, Tutku Soyer, Pelin Özlem Şimşek-Kiper, Gülen Eda Utine, Gökhan Tunçbilek, Koray Boduroğlu, Mehmet Alikaşifoğlu

“…For this purpose, primary skin fibroblast cultures obtained from 3 individuals with Apert syndrome and 3 controls without craniosynostosis were compared by transcriptome microarray, GeneChip Human Genome U133 Plus 2.0. …”
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Transcriptome Comparison between Resistant and Susceptible Soybean Cultivars in Response to Inoculation of Phytophthora sojae by Sangrea Shim, In-Jeong Kang, Hee Jin You, Hangil Kim, Sungwoo Lee

“…In this study, we performed a comparative transcriptomic analysis of Socheong2 and Daepung, two Korean soybean varieties identified as resistant and susceptible to P. sojae isolate 2457, respectively. …”
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Survey of transcriptome analyses of hippocampal neurogenesis with focus on adult dentate gyrus stem cells by Laura Micheli, Maurizia Caruso, Giorgio D’Andrea, Daniel Volpe, Manuela Ceccarelli, Felice Tirone

“…This suggests an important role of these cells in human neurogenesis and hence interspecies differences in the neurogenic process dynamics. This review is focused on transcriptomic studies that have faced these and other NSC issues by analyzing developmental trajectories of neural cells and NSCs gene expression profiles in specific experimental settings of hippocampal neurogenesis, and also in mouse models with deletion or overexpression of specific genes to reproduce neural pathologies.…”
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Transcriptomic profiling of cumulus cells reveals dysregulated genes and pathways in PCOS-related infertility by Akeem Babatunde Sikiru, Nurulfiza Mat Isa, Kasim Sakran Abass, Muibat Adesola Adeniran, Stephen Sunday Acheneje Egena, Karimot Akinola

“…Method This study investigates transcriptomic differences in cumulus cells between PCOS and non-PCOS women using high-throughput RNA sequencing data obtained from the NCBI Gene Expression Omnibus (GEO) database (accession number: GSE277906). …”
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Unravelling the transcriptomic landscape of primary lymphocytic scarring alopecias: systematic review and meta-analysis by Irene Rivera-Ruiz, Irene Rivera-Ruiz, Benjamin Ungar, Viviana Dávila-Flores, Jesús Gay-Mimbrera, Pedro J. Gómez-Arias, Pedro J. Gómez-Arias, Miguel Juan-Cencerrado, Miguel Juan-Cencerrado, Carmen Mochón-Jiménez, Carmen Mochón-Jiménez, Esmeralda Parra-Peralbo, Beatriz Isla-Tejera, Beatriz Isla-Tejera, Teresa López-Viñau López, Teresa López-Viñau López, Emma Guttman-Yassky, Juan Ruano, Juan Ruano

“…Despite overlapping histopathology, their molecular differences remain poorly defined. We performed the first systematic review and transcriptomic meta-analysis of human scalp biopsies in PLSAs (PROSPERO: CRD42024559969), following PRISMA 2020 guidelines. …”
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Integrating transcriptomics and proteomics to analyze new regulatory genes related to rice grain development by Zhixuan Du, Qitao Su, Haihui Fu, Dahu Zhou, Linjuan Ouyang, Junru Fu, Haohua He

“…This observation indicates that the differences in grain size between the large-grain line AD3 and the small-grain line AD148 result from distinct biological processes occurring both during the early stages of glume development and the grain filling stage. …”
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