Transcriptome-wide dynamics of m6A methylation in ISKNV and Siniperca chuatsi cells infected with ISKNV by Qijin Miao, Jing Jiang, Siyou Huang, Jie Gao, Qingqing Liu, Rui Zheng, Yiling Kang, Changjun Guo, Jianguo He, Junfeng Xie

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The archaeal class Nitrososphaeria is a key component of the reproductive microbiome in sponges during gametogenesis by Marta Turon, Vasiliki Koutsouveli, María Conejero, Sergi Taboada, Aida Verdes, José María Lorente-Sorolla, Cristina Díez-Vives, Ana Riesgo

“…Most studies have concentrated on the proportion of the microbiome transmitted from parents to offspring, providing little evidence of the putative microbial role during gametogenesis in sponges. …”
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Mechanisms of flavonoids in quinoa’s response to flooding stress in grain filling stage by Guofei Jiang, Xuqin Wang, Qingwen Jiang, Yutao Bai, Lingyuan Zhang, Ping Zhang, Junna Liu, Li Li, Hanxue Li, Liubin Huang, Shan Zhang, Peng Qin

“…Genes related to flavonoids in the transcriptome were significantly enriched in both GO and KEGG. …”
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Unveiling the Regulatory Mechanism of Tibetan Pigs Adipogenesis Mediated by WNT16: From Differential Phenotypes to the Application of Multi-Omics Approaches by Qiuyan Huang, Kunli Zhang, Fanming Meng, Sen Lin, Chun Hong, Xinming Li, Baohong Li, Jie Wu, Haiyun Xin, Chuanhuo Hu, Xiangxing Zhu, Dongsheng Tang, Yangli Pei, Sutian Wang

“…This cross-level regulatory mechanism of “phenotype detection–multi-omics analysis–gene function research” highlighted WNT16 as a potential key regulator of site-specific fat deposition, providing new molecular targets for optimizing meat quality through nutritional regulation and genetic modification.…”
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Transcriptomic miRNA and mRNA signatures in primary prostate cancer that are associated with lymph‐node invasion by Matias A. Bustos, Kelly K. Chong, Yoko Koh, SooMin Kim, Eleanor Ziarnik, Romela I. Ramos, Gianna Jimenez, David L. Krasne, Warren M. Allen, Timothy G. Wilson, Dave S. B. Hoon

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Deciphering cancer therapy resistance via patient-level single-cell transcriptomics with CellResDB by Tianyuan Liu, Huiyuan Qiao, Liping Ren, Xiucai Ye, Quan Zou, Yang Zhang

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Single cell transcriptome profiling of immune tissues from germ-free and specific pathogen-free piglet by Jinwei Zhang, Chuang Tang, Yan Liu, Jing Sun, Xiaokai Li, Keren Long, Fanli Kong, Shuangshuang Chen, Hao Liang, Yuchun Ding, Mingzhou Li, Li Shen, Junbo Ge, Jideng Ma, Liangpeng Ge

“…As the first single-cell transcriptomics dataset for immune tissue of GF and SPF piglet, this provides a valuable data resource for the study of commensal microbe-host immunity regulation.…”
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Causal Biological Network Model for Inflammasome Signaling Applied for Interpreting Transcriptomic Changes in Various Inflammatory States by Hasmik Yepiskoposyan, Manuel C. Peitsch, Marja Talikka

“…The scoring inferred pathway activation leading to NLRP3 inflammasome activation in these diverse conditions, demonstrating that the CBN model provides a platform for interpreting transcriptomic data in the context of inflammasome activation.…”
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Novel cancer subtyping method guided by tumor-normal sample in latent space of transcriptomic variational autoencoder by Hongzhi Wang, Yu Zhang, Dandan Zhang, Min Luo

“…Current tumor omics analyses often focus exclusively on tumor samples, overlooking the valuable insights that normal tissues can provide. To address this gap, we introduce VaDTN (Variational Autoencoder–Derived Tumor-to-Normal), a pan-cancer framework that integrates transcriptomic data from both tumor and normal samples into a unified latent space. …”
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Spatial transcriptomic analysis drives PET imaging of tight junction protein expression in pancreatic cancer theranostics by James Wang, Jai Woong Seo, Aris J. Kare, Martin Schneider, Mallesh Pandrala, Spencer K. Tumbale, Marina N. Raie, Gokce Engudar, Nisi Zhang, Yutong Guo, Xiaoxu Zhong, Sofia Ferreira, Bo Wu, Laura D. Attardi, Guillem Pratx, Andrei Iagaru, Ryan L. Brunsing, Gregory W. Charville, Walter G. Park, Katherine W. Ferrara

“…Abstract Molecular imaging using positron emission tomography (PET) provides sensitive detection and mapping of molecular targets. …”
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Transcriptome analysis of ovarian cancer uncovers association between tumor-related inflammation/immunity and patient outcome by Jingfang Wang, Wenrui Zhu, Xia Li, Yuanyuan Wu, Wenhui Ma, Yangzhou Wang, Weihong Zhao, Fang Wei, Wenhao Wang

“…., tumor immunotherapy has provided new opportunities for the treatment of ovarian cancer.MethodsThis study used comprehensive transcriptome analysis across multiple databases to gather gene transcripts and clinical features of normal ovarian samples and tissue samples from ovarian cancer. …”
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MENGA: A New Comprehensive Tool for the Integration of Neuroimaging Data and the Allen Human Brain Transcriptome Atlas. by Gaia Rizzo, Mattia Veronese, Paul Expert, Federico E Turkheimer, Alessandra Bertoldo

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High-throughput sequencing and de novo assembly of Brassica oleracea var. Capitata L. for transcriptome analysis. by Hyun A Kim, Chan Ju Lim, Sangmi Kim, Jun Kyoung Choe, Sung-Hwan Jo, Namkwon Baek, Suk-Yoon Kwon

“…Hence, the construction of reliable transcriptomic data based on high-throughput sequencing technologies is needed to enhance our understanding of cabbage and provide genomic information for future work.…”
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Mapping dynamic regulation of gene expression using single-cell transcriptomics and application to complex disease genetics by Hanna Abe, Phillip Lin, Dan Zhou, Douglas M. Ruderfer, Eric R. Gamazon

“…Summary: Single-cell transcriptome data can provide insights into how genetic variation influences biological processes involved in human physiology and disease. …”
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Transcriptome Analysis Between Parents and Offspring Revealed the Early Salt Tolerance Mechanism of Rice NGY1 by Cheng Li, Kai Lu, Wen-Hua Liang, Tao Chen, Shu Yao, Lei He, Xiao-Dong Wei, Ling Zhao, Li-Hui Zhou, Chun-Fang Zhao, Qing-Yong Zhao, Zhen Zhu, Cai-Lin Wang, Ya-Dong Zhang

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A systematic regulatory network related to bulbil formation in Lilium lancifolium based on metabolome and transcriptome analyses by Ruiyi Ma, Yan Zhang, Jun Zhao, Yang Zheng, Li Xue, Jiajun Lei

“…This study not only provided more information about the differentially expressed genes and metabolites through transcriptome and metabolomics analyses, but also provided a clearer understanding of the effect of hormones on bulbil formation in lily.…”
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Integrative transcriptomics and metabolomics reveal neuroendocrine-lipid crosstalk and adenosine signaling in broiler under heat stress by Bingxing An, Peihao Liu, Zhirui Yang, Fan Ying, Dawei Liu, Jie Wen, Guiping Zhao

“…These results could provide an effective theoretical basis of the preventive and treatment measures for HS.…”
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Transcriptome sequencing revealed the regulation of stem internode length associated with mechanical harvesting in three tea varieties by Xiaozeng Mi, Xiaozeng Mi, Dahe Qiao, Dahe Qiao, Chun Yang, Chun Yang, Juan Chen, Sihui Liang, Sihui Liang, Yan Guo, Yan Guo

“…IntroductionInternode length of tea plant is one of the key traits affecting the mechanical harvesting effect, but there are relatively few reports on their molecular regulatory.MethodsTranscriptome sequencing (RNA-seq) was performed on it in order to explain its molecular mechanism. …”
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Comparative transcriptome analysis of the effect of different heat shock periods on the unfertilized ovule in watermelon (Citrullus lanatus) by Ying-chun ZHU, De-xi SUN, Yun DENG, Guo-lin AN, Wei-hua LI, Wen-jing SI, Jun-pu LIU, Xiao-wu SUN

“…The results provide new information on the complex relationship between in vitro gynogenesis and temperature. …”
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Transcriptome analysis reveals age-specific growth characteristics in the rumen of Hanwoo (Korean native cattle) steers by Yejee Park, Sunsik Jang, Han-Ha Chai, Ju-Whan Son, Dajeong Lim, Woncheoul Park

“…Proper feed management, considering the rumen’s function, is essential for optimal growth. Transcriptome analysis helps identify genes associated with growth and provides insights for cattle breeding and management practices. …”
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