Transcriptomic Analyses Reveal Light-Induced Anthocyanin Accumulation in <i>Lycium ruthenicum</i> Murray by Shengrong Chen, Tao He, Wenyi Gu, Ruimin Li, Yinyan Qi

“…A proposed model has been developed to elucidate the mechanism by which light controls the biosynthesis of anthocyanin, providing insights into light signal regulation. Our findings provide data to improve the understanding of light-induced anthocyanin accumulation in <i>L. ruthenicum</i> berries.…”
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Joint analysis of transcriptome and metabolome on the accumulation mechanism of flavonoids in quinoa seedlings under flooding stress by Xuqin Wang, Ping Zhang, Zhiwei Qin, Guofei Jiang, Yutao Bai, Lingyuan Zhang, Junna Liu, Li Li, Hanxue Li, Liubin Huang, Jie Yang, Yuming Xie, Jianlong Zhou, Huanyao Xia, Peng Qin

“…Methods We used one highly resistant and two sensitive lines as experimental materials, and combined metabolomic and transcriptomic associations as well as WGCNA to describe and analyze in detail the accumulation of flavonoids in quinoa seedlings under flooding stress in three quinoa lines. …”
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Comprehensive analysis of transcriptome and metabolome identified the key gene networks regulating fruit length in melon by Qingtao Wang, Lingli Tang, Yuhua He, Yongyang Xu, Jian Zhang, Weihu Kong, Keyun Hu, Jordi Garcia-Mas, Marta Pujol, Guangwei Zhao

“…Results In this study, we investigated the gene network regulating fruit morphology in melons utilizing transcriptome profile and a co-expression pattern-based approach. …”
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An Integrated Approach Involving Metabolomics and Transcriptomics Reveals Arsenic-Induced Toxicity in Human Renal Cells by Lin Rong, Xinxin Liang, Xingfang Zhang, Yajun Qiao, Guoqiang Li, Yuancan Xiao, Hongtao Bi, Lixin Wei

“…Overall, the present study provided comprehensive insights into the metabolic and transcriptional alterations in human renal cells in response to arsenic exposure, providing a referable scientific basis for subsequent arsenic-induced nephrotoxicity studies.…”
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RNAcare: integrating clinical data with transcriptomic evidence using rheumatoid arthritis as a case study by Mingcan Tang, William Haese-Hill, Fraser Morton, Carl Goodyear, Duncan Porter, Stefan Siebert, Thomas D. Otto

“…Users, including clinicians with a general knowledge of transcriptomics, however, who may have limited programming experience, are increasingly seeking tools that go beyond traditional analysis. …”
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Flavor, Lipid, and Transcriptomic Profiles of Chinese Wagyu Beef Cuts: Insights into Meat Quality Differences by Tianliu Zhang, Tingting Wang, Yanhao Gao, Jiashun Sheng, Hossam E. Rushdi, Wentao Li, Yu Sun, Tong Fu, Feng Lin, Tengyun Gao, Shenhe Liu

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Comprehensive analysis of histophysiology, transcriptomics and metabolomics in goslings exposed to gossypol acetate: unraveling hepatotoxic mechanisms by Jun Yu, Jun Yu, Haiming Yang, Jian Wang, Zixin Huang, Shi Chen, Hongchang Zhao, Jun Wang, Zhiyue Wang

“…These findings highlight the vulnerability of mitochondria and critical metabolic pathways, providing insights into the molecular mechanisms of GA toxicity and guiding future studies on mitigating GA-induced liver damage in goslings.…”
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The transcriptome reveals the potential mechanism of 20E terminating diapause in cotton bollworm, Helicoverpa armigera by Zhaohong Ni, Yan Li, Shunchao Xia, Zhaolang Teng, Jianjun Guo, Jing Liao, Haiyin Li

“…Subsequently, RNA-Seq was employed to construct a comprehensive transcriptome map of the 20E-induced termination of diapause. …”
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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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Screening and validation of key genes involved in castration-resistant prostate cancer based on transcriptomics sequencing by Guangquan Tong, Xiaomeng Jing, Yuning Yang, Xiaowei Wang, Junlin Lu, Jingyi Hu, Yang Wang, Farra Aidah Jumuddin, Wenjing Zhang, Yuesheng Lv

“…Our research findings suggest that S100A6 may serve as a molecular marker or therapeutic target associated with castration resistance in prostate cancer, providing new insights into the molecular basis of this disease.…”
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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

“…Results Histological and transcriptomic analyses identified the period between 90 and 120 dph as critical for sex differentiation in silver pomfret. …”
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Integrative Analysis of Transcriptomic and Metabolomic Profiles Uncovers the Mechanism of Color Variation in the Tea Plant Callus by Mengna Xiao, Yingju Tian, Ya Wang, Yunfang Guan, Ying Zhang, Yuan Zhang, Yanlan Tao, Zengquan Lan, Dexin Wang

“…Furthermore, this study investigated the molecular mechanisms underlying callus color changes using transcriptomic and metabolomic approaches. Based on transcriptome analysis, it was revealed that photosynthesis and flavonoid biosynthesis pathways were significantly enriched. …”
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Disparate and shared transcriptomic signatures associated with cortical atrophy in genetic behavioral variant frontotemporal degeneration by Ting Shen, Jacob W. Vogel, Vivianna M. Van Deerlin, EunRan Suh, Laynie Dratch, Jeffrey S. Phillips, Lauren Massimo, Edward B. Lee, David J. Irwin, Corey T. McMillan

“…Methods We employed an integrative imaging transcriptomics approach to identify both disparate and shared transcriptomic signatures associated with cortical thickness in bvFTD with C9orf72 repeat expansions or pathogenic variants in GRN or MAPT. …”
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Transcriptome analysis of multiple tissues and identification of tissue-specific genes in Lueyang black-bone chicken by Pan Li, Yufei Yang, Bo Ning, Yingmin Tian, Ling Wang, Wenxian Zeng, Hongzhao Lu, Tao Zhang

“…In this study, the gene expression profiles of 9 major tissues of Lueyang black-bone chicken were successfully constructed by transcriptome sequencing technology. Through in-depth analysis of transcriptome data, a total of 10 housekeeping genes (HKGs) and 87 marker genes (MGs) were identified. …”
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Transcriptome and Metabolome Insights into Key Genes Regulating Fat Deposition and Meat Quality in Pig Breeds by Suthar Teerath Kumar, Yunlong Zheng, Jing Xu, Ziyi Zhao, Qi Zhang, Yunpeng Zhang, Min Li, Hong Zou, Riaz Muhammad Azeem, Wu-Sheng Sun, Yuan Zhao, Shu-Min Zhang

“…Fatty acid (FA) analysis identified 15 significant FAs in the LWLDP, with docosahexaenoic acid (DHA) in the SBP, while amino acid (AA) analysis revealed no breed-based differences. Transcriptome analysis identified 134 upregulated and 362 downregulated genes in the SBP. …”
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De novo transcriptome assembly and analysis of differential gene expression in response to drought in European beech. by Markus Müller, Sarah Seifert, Torben Lübbe, Christoph Leuschner, Reiner Finkeldey

“…Here, we used RNA-seq to provide the first drought stress-related transcriptome of beech. …”
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Combined endurance and resistance exercise training alters the spatial transcriptome of skeletal muscle in young adults by Michael J. Stec, Zachary A. Graham, Qi Su, Christina Adler, Min Ni, Valerie Le Rouzic, David R. Golann, Patrick J. Ferrara, Gabor Halasz, Mark W. Sleeman, Kaleen M. Lavin, Timothy J. Broderick, Marcas M. Bamman

“…Additionally, integration of human muscle single cell RNAseq data identified an exercise-induced shift in interstitial cell populations coincident with angiogenesis. Overall, these data provide a unique spatial molecular profiling resource for exploring muscle adaptations to exercise, and provide a pipeline and rationale for future studies in human muscle.…”
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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

“…Results Phylogenomic analysis of 37 Spirostomum specimens (25 newly generated transcriptomes and 12 from GenBank) and 265 protein-coding genes provides robust insight into the evolutionary relationships among Spirostomum species. …”
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Dual probe ligation in situ hybridization with rolling-circle amplification for high-plex spatial transcriptomics by Sarah E. Maguire, Joel Credle, Elizabeth M.W. Bertelson, Sunny Lee, Boyoung Cha, Dan Xie, Greg Kirk, Debjit Ray, Logan George, Aditya Suru, Alexandre Maalouf, Chiseko Ikenaga, Thomas Lloyd, Nicolas J. Llosa, H. Benjamin Larman

“…Combined with LISH-seq and LISH-QC, the LISH-LnR methodology provides a powerful toolkit for spatial transcriptomics.…”
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Identification and analysis of bHLH transcription factor family in red raspberry based on transcriptome sequencing by HE Zhimin1,2, ZHANG Junxin1,2, YU Liping1,2, HU Kang1,2, JI Fengqi1,2, HUANG Tiran1,2, YANG Mingfeng1,2*, MA Lanqing1,2

“…To investigate the role of bHLH transcription factor in the growth and development of red raspberry and the synthesis of raspberry ketone, members of the red raspberry bHLH gene family were identified and bioinformatics analysis of these genes were performed based on transcriptome sequencing of two red raspberry fruits, ‘Polka' and ‘Orange Legend'. …”
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