Transcriptome analysis of archived tumors by Visium, GeoMx DSP, and Chromium reveals patient heterogeneity by Yixing Dong, Chiara Saglietti, Quentin Bayard, Almudena Espin Perez, Sabrina Carpentier, Daria Buszta, Stephanie Tissot, Rémy Dubois, Atanas Kamburov, Senbai Kang, Carla Haignere, Rita Sarkis, Sylvie Andre, Marina Alexandre Gaveta, Silvia Lopez Lastra, Nathalie Piazzon, Rita Santos, Katharina von Loga, Caroline Hoffmann, George Coukos, Solange Peters, Vassili Soumelis, Eric Yves Durand, Laurence de Leval, Raphael Gottardo, Krisztian Homicsko, Elo Madissoon

“…Abstract Recent advancements in probe-based, full-transcriptome technologies for FFPE tissues, such as Visium CytAssist, Chromium Flex, and GeoMx DSP, enable analysis of archival samples, facilitating the generation of data from extensive cohorts. …”
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Integrating transcriptomics and hybrid machine learning enables high-accuracy diagnostic modeling for nasopharyngeal carcinoma by Hehe Wang, Junge Zhang, Peng Cheng, Lujie Yu, Chunlin Li, Yaowen Wang

“…This study aimed to develop robust machine learning (ML)-driven diagnostic models and identify key biomarkers through integrated analysis of multi-cohort transcriptomic data. Methods Seven NPC transcriptomic datasets (GSE12452, GSE40290, GSE53819, and GSE64634 were merged to form the training cohort, while GSE13597, GSE34573, and GSE61218 served as independent external validation sets) were integrated and preprocessed using ComBat for batch effect correction. …”
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Transcriptome sequencing and anthocyanin metabolite analysis involved in leaf red color formation of Cinnamomum camphora by Xinxin Wu, Yan Li, Tong Du, Li Kang, Baolei Pei, Weibing Zhuang, Fang Tang

“…In this study, green leaf (GL), color turning red leaf (RL) and whole red leaf (WRL) were obtained to measure pigment contents, while GL and RL were analyzed for transcriptomic alterations. …”
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Cytological, Phytohormone, and Transcriptomic Analyses Reveal the Key Genes and Pathways Involved in Melon Fruit Cracking by Rong Fan, Bin Liu, Xiaoyu Duan, Meihua Li, Yongbing Zhang, Xuejun Zhang, Guozhi Hu, Yong Yang

“…R2 has small, tightly packed epidermal cells with a thick cuticle, while R6 has larger, more loosely arranged epidermal cells and a significantly thinner cuticle. …”
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The Causal Effects Between Circulating Inflammatory Proteins and Osteoarthritis: A Mendelian Randomization and Transcriptomic Analysis by Lin S, Wu C, Pan Y

“…The GWAS summary data for OA were derived from The Musculoskeletal Knowledge Portal, while the GWAS summary data for 91 circulating inflammatory proteins were obtained from a recently published study. …”
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Single-cell transcriptomics unveils leukocyte heterogeneity in the gills of Larimichthys crocea in response to parasitic infection by Qiuhua Li, Qiuhua Li, Meiyan Wang, Chenhao Li, Ngoc Tuan Tran, Jingqun Ao, Shengkang Li, Xinhua Chen

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Transcriptomic and proteomic profiling identifies feline fibrosarcoma as clinically amenable model for aggressive sarcoma subtypes by Mikiyo Weber, Daniel Fuchs, Amiskwia Pöschel, Erin Beebe, Zuzana Garajova, Armin Jarosch, Laura Kunz, Witold Wolski, Lennart Opitz, Franco Guscetti, Mirja C. Nolff, Enni Markkanen

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Integrated Analysis of the Metabolome and Transcriptome During Apple Ripening to Highlight Aroma Determinants in Ningqiu Apples by Jun Ma, Guangzong Li, Yannan Chu, Haiying Yue, Zehua Xu, Jiaqi Wu, Xiaolong Li, Yonghua Jia

“…Our findings revealed substantial transcriptomic and metabolomic divergence across carotenoid, terpenoid, and fatty acid metabolic pathways. …”
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Integrated Analysis of DNA Methylome and Transcriptome Reveals Regulatory Mechanism in the Longissimus Dorsi of Duroc Pigs by Shiyin Li, Yarui Gao, Lixia Ma, Wei Chen, Zhao Ma, Zhanchi Ren, Yunzhou Wang, Yongqing Zeng

“…In this study, we analyzed the DNA methylome and transcriptome of the longissimus dorsi muscle (LDM) in Duroc pigs with varying growth rates. …”
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Exogenous Gibberellin Delays Postharvest Leaf Senescence in Pak Choi by Modulating Transcriptomic and Metabolomic Profiles by Dan Wang, Xiuyun Zhao, Tongbing Su, Weihong Wang, Xiaoyun Xin, Bin Zhang, Deshuang Zhang, Yangjun Yu, Zhongjiang Wang, Fenglan Zhang, Linyi Zhou, Peirong Li, Shuancang Yu

“…This study, through a combination of transcriptomic and metabolomic analyses, investigated the effect of exogenous GA on postharvest leaf senescence in pak choi. …”
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Transcriptomics combined with physiological analysis provides insights into the mechanism of resistance to Coleosporium bletiae in Bletilla striata by Qiao Liu, Xi Lu, Qiaofen Wu, Zhibiao Lu, Renjun Qin, Kui Huang, Xun Zou, Ke Xia, Yanni Yang, Shuo Qiu

“…However, its cultivation faces significant challenges from leaf rust disease caused by Coleosporium bletiae, which causes substantial yield losses.MethodsTo investigate host resistance mechanisms, we compared rust-resistant and susceptible B. striata accessions through integrated transcriptomic and physiological analyses.Results and discussionPhenotypic observations revealed that while both resistant and susceptible plants developed rust spores by 2 days post-inoculation (dpi), the resistant accession exhibited a significantly slower progression of spore stack formation and lesion expansion on abaxial leaf surfaces over time. …”
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Comparative transcriptomics analysis of the Oleidesulfovibrio alaskensis G20 biofilms grown on copper and polycarbonate surfaces by Priya Saxena, Dipayan Samanta, Payal Thakur, Vinoj Gopalakrishnan, Rajesh K. Sani

“…Sulfate-reducing bacterial (SRB) biofilms are prevalent across diverse environments, playing key roles in biogeochemical sulfur cycling while also contributing to industrial challenges such as biofouling and biocorrosion. …”
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Transcriptome analysis reveals the sex-switching mechanism of juvenile hermaphroditism in silver pomfret (Pampus argenteus) by Yaya Li, Jiabao Hu, Chongyang Wang, Man Zhang, Youyi Zhang, Yuanbo Li, Mengke Tang, Chunlai Qin, Zukang Feng, Shanliang Xu, Xiaojun Yan, Xubo Wang, Haimin Chen, Yajun Wang

“…RT-qPCR validated the sequencing results, while immunofluorescence (IF) examined the expression of related genes in testes and ovaries. …”
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Obesity impact on leukocyte telomere shortening and immune aging assessed by Mendelian randomization and transcriptomics analysis by Zhijun Feng, Jiacheng Li, Huimin Zhang, Shupeng Liu, Yinghui Wang, Meijuan Zhou, Zhenhua Ding, Lin Xiao

“…Abstract Obesity and aging are key research topics in contemporary biomedical science. While studies have explored the effects of obesity on various health indicators, the precise mechanisms through which obesity may affect leukocyte telomere length (LTL)-and whether this impact contributes to accelerated immune cell senescence-remain unclear and warrant further investigation. …”
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Transcriptome analysis provides insights into aril development regulated gene network in lychee, longan, and rambutan by Suyan Wan, Fei Dong, Yaying Ma, Yuan Yao, Yang Wang, Yawen Xu, Ray Ming, Wenping Zhang

“…OrthoFinder identified species-specific and shared differentially expressed genes (DEGs), while functional enrichment analyses (GO, KEGG) and transcriptional network modeling elucidated regulatory pathways. …”
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Mining, validating, and quantifying circular RNA transcriptome from total RNA as a biomarker or target by Tan Ze Wang, Raj Kumar Thapa, Frank Yu, Ayesha Warsi, Kassie Rong, Pious Jose, Tahereh Kashkoulinejad-Kouhi, Phyo Wei Win, Christina A. Castellani, Tina Mele, Xiufen Zheng

“…TopHat was found to be the most sensitive aligner while MapSplice was found to be the most accurate. …”
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Transcriptomic and electrophysiological alterations underlying phenotypic variability in SCN1A-associated febrile seizures by Stefania Scalise, Alessandro Gaeta, Elio Aprigliano, Valeria Lucchino, Raffaele Covello, Mariagrazia Talarico, Barbara Puccio, Pietro Hiram Guzzi, Pierangelo Veltri, Antonio Gambardella, Lilian Juliana Lissner, Alessandra Morano, Pierangelo Cifelli, Veronica Alfano, Eleonora Palma, Gerardo Perozziello, Gabriele Ruffolo, Giovanni Cuda, Elvira Immacolata Parrotta

“…Abstract Febrile seizures (FS) are a common childhood neurological condition triggered by fever in children without prior neurological disorders. While generally benign, some individuals, particularly those with complex FS or genetic predispositions, may develop epilepsy or other neurological comorbidities. …”
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Phylogeny and species delimitation of ciliates in the genus Spirostomum (class Heterotrichea) using single-cell transcriptomes by Shahed Uddin Ahmed Shazib, Auden Cote-L’Heureux, Ragib Ahsan, Sergio A. Muñoz-Gómez, JunMo Lee, Laura A. Katz, Mann Kyoon Shin

“…We evaluated the utility of the transcriptomic data by constructing species trees using concatenation and coalescent-based methods. …”
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Dynamic transcriptome and metabolome analyses of two sweet corn lines under artificial aging treatment by Zili Zhang, Ruichun Yang, Lei Gao, Shilin Huang, Feng Jiang, Qingchun Chen, Pengfei Liu, Faqiang Feng

“…The identical enriched KEGG pathways were observed in the 3d vs 6d comparison for K107 and 0d vs 6d comparison for L155, indicating a slower transcriptomic response in the aging-tolerance line. DEGs at 0 days between the two lines had been enriched in the “Terpenoid backbone biosynthesis” and “Ribosome” pathways, while at 6 days, the enrichment pathway were “Sulfur metabolism”, “Linoleic acid metabolism”, and “Plant hormone signal transduction”. …”
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Comparative Transcriptomic Analyses of Anthocyanin Biosynthesis Genes in Eggplant Under Low Temperature and Weak Light by Baoying Shen, Hongqi Wu, Xinxin Xie, Bo Zhao, Peiqiang Chen, Deyong Ao, Heli Pan, Biying Lin

“…The anthocyanin content in eggplants increased under low temperature and the combination of low temperature and weak light treatments, while it decreased under weak light. KEGG analysis showed that three pathways, namely phenylpropanoid biosynthesis, flavonoid biosynthesis, and anthocyanin biosynthesis, were involved in the anthocyanin biosynthesis of eggplants. …”
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