Comprehensive multi-omics and biochemical analysis to elucidate the molecular response mechanisms of gill and kidney tissues under acute salinity stress in Pseudobagras ussuriensis by Yu Liu, Libo Gu, Jun Zhao, Mengzhu Liu, Ke Wang, Qingbo Zhou, Yang Cao, Ruyi Hu, Weiwei Wang, Qing Liu

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Transcriptomic profiles reveal hormonal regulation of sugar-induced stolon initiation in potato by Xiaoqing Wang, Kaifeng Zheng, Tiancang Na, Guangji Ye, Shengcheng Han, Jian Wang

“…Using a combination of in vitro culture, transcriptomics, gene expression analysis, and biochemical approaches, we investigated the contribution of sucrose (3% or 8%) on potato seedling stem nodes and stolon initials through phenotypic observation, RNA sequencing (RNA-seq), comparison of expression patterns, and hormone quantification. …”
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Understanding Host–Pathogen Interactions in Congenital Chagas Disease Through Transcriptomic Approaches by Tatiana M. Cáceres, Luz Helena Patiño, Juan David Ramírez

“…Chagas disease, caused by <i>Trypanosoma cruzi</i>, is a parasitic zoonosis with significant health impacts, particularly in Latin America. While traditionally associated with vector-borne transmission, increased migration has expanded its reach into urban and non-endemic regions. …”
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Integrating Deep Learning and Transcriptomics to Assess Livestock Aggression: A Scoping Review by Roland Juhos, Szilvia Kusza, Vilmos Bilicki, Zoltán Bagi

“…The two innovative tools of deep learning-based video analysis and transcriptomic profiling have recently appeared to aid the understanding and monitoring of such behaviors. …”
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Rapid Alterations in Perirenal Adipose Tissue Transcriptomic Networks with Cessation of Voluntary Running. by Gregory N Ruegsegger, Joseph M Company, Ryan G Toedebusch, Christian K Roberts, Michael D Roberts, Frank W Booth

“…From the 10th to 11th week of age, one group of rats had continued wheel access, while the other group had one week of wheel locking. …”
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Mechanisms of Microctis Folium in Hyperlipidemia: Integrating Serum Pharmacochemistry, Network Pharmacology, and Transcriptomics by Xiao G, Wu G, Liu Y, Chen W, Zeng Z, Li S, Li Y, Bi X

“…Merr, hyperlipidemia, network pharmacology, serum pharmacochemistry, transcriptomics…”
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Integrated analysis of single-cell, spatial and bulk RNA-sequencing identifies a cell-death signature for predicting the outcomes of head and neck cancer by Yue Pan, Lei Fei, Shihua Wang, Hua Chen, Changqing Jiang, Hong Li, Changsong Wang, Yao Yang, Qinggao Zhang, Yongwen Chen

“…Finally, samples from laryngeal squamous cell cancer (LSCC) were conducted by spatial transcriptomics (ST) to further validate the results of CDRscore model.ResultsT cells from HNC patients manifested the highest levels of cell death while HPV infection attenuates malignant cell death based on single-cell atlas. …”
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Transcriptome signature in the blood of neuromyelitis optica spectrum disorder under steroid tapering by Ryohei Yamamura, Makoto Kinoshita, Yoshiaki Yasumizu, Yoshiaki Yasumizu, Yoshiaki Yasumizu, Tomohiro Yata, Keigo Kihara, Daisuke Motooka, Daisuke Motooka, Naoyuki Shiraishi, Yasuko Sugiyama, Shohei Beppu, Hisashi Murata, Naoshi Koizumi, Itsuki Sano, Toru Koda, Tatsusada Okuno, Hideki Mochizuki

“…Weighted gene co-expression network analysis identified modules that correlated with steroid dosage, and the modules inversely correlated with steroid dosage were enriched in monocytes, with marked immune signature of interferon pathway.ConclusionThis study identified peripheral blood transcriptome signatures that could lead to the identification of clinically relevant NMOSD disease activity biomarkers, and further highlights the pivotal role of interferon and IL-10 signaling in NMOSD.…”
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Single-cell transcriptomics uncovers key immune drivers of vaccine efficacy in cattle by Annaleise Wilson, Pâmela A. Alexandre, Aaron M. Brice, Brad C. Hine, Aaron Ingham, Thibault P. R. A. Legrand, Caroline Royle, Dominic Niemeyer, Antonio Reverter, Stuart E. Denman, Ryan J. Farr

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ProbC: joint modeling of epigenome and transcriptome effects in 3D genome by Emre Sefer

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Combined Genomic and Transcriptomic Screening of Candidate Genes for Asymmetric Oviduct Development in Hens by Ruijie Li, Xiang Song, Xiao Lin, Mingli Deng, Yin Liu, Tuoyu Geng, Daoqing Gong, Minmeng Zhao, Long Liu

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Comparative transcriptomics of atrazine-tolerant and sensitive alfalfa varieties under atrazine stress by Yingao Li, Chunyang Dong, Zeshan Zulfiqar, Haojie Wang, Jiading Lu, Xiaoxia Zhang, Jun Li, Yinghua Shi, Chengzhang Wang, Xiaoyan Zhu, Hao Sun

“…However, atrazine, a widely used herbicide, negatively impacts the growth and yield of alfalfa due to its residual presence in the environment. Transcriptomic analysis was performed to investigate the differences in tolerance and uncover the potential molecular regulatory mechanisms between the tolerant variety JN5010 and the sensitive variety WL363 when subjected to atrazine stress, using RNA-seq on pooled samples. …”
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Impact of perinatal factors on T cells and transcriptomic changes in preterm infant brain injury by Xiaoli Zhang, Yu Yang, Yiran Xu, Liuji Chen, Ming Niu, Jinjin Zhu, Shan Zhang, Yanan Wu, Bingbing Li, Lingling Zhang, Juan Song, Falin Xu, Dan Bi, Xin Zhao, Changlian Zhu, Xiaoyang Wang

“…No significant associations were found between Vδ2+ T cell proportions and perinatal factors other than gestational age or brain injury. Blood transcriptome analysis revealed 173 differentially expressed genes, characterized by downregulated interferon signaling and upregulated antimicrobial and neutrophil pathways in infants with brain injury. …”
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Multi-tissue transcriptomic characterization of endogenous retrovirus-derived transcripts in Capra hircus by Ming-Di Li, Ming-Di Li, Hu-Rong Li, Shao-Hui Ye

“…TE-derived reads account for 10% of the transcriptome and their abundance are comparable in various goat tissues, while expression of ERVs are variable among tissues. …”
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Integration of metabolomics and transcriptomics analyses reveals the effects of nano-selenium on pak choi by Yanyan Wang, Peiheng Sun, Mingying Nie, Jianyun Zhan, Liu Huang, Junda Wu, Jie Zhang, Xiaowu He, Na Li, Longsong Hu, Shiyu Liu, Chengfu Yuan, Changming Zhou, Guangjie Chen, Jialong Huang, Xiaofei Li

“…Therefore, this study aims to investigate the impact of nano-selenium on pak choi through an integrated analysis of transcriptome and metabolome. Specifically, we examined the effects of different concentrations of nano-selenium (0, 5, 10 and 20 mg L−1) on the growth and nutritional quality of Suzhouqing. …”
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Novel kinetic and developmental transcriptomic pan-stress responses by embryonic stem cells by Aditi Singh, Ximena Lu Ruden, Wen Tang, Awoniyi Olumide Awonuga, Douglas Mark Ruden, Steven James Korzeniewski, Elizabeth Ella Puscheck, Hao Feng, Daniel Allen Rappolee

“…ESC were exposed to control stimuli and diverse stressors at previously characterized risk levels for growth, mimicking miscarriage risk exposures, then subjected to transcriptomic analysis via RNA sequencing. Surprisingly, we identify a large, substantial set of significantly-changing genes—termed pan-stress genes that also exhibited concordant changes in directionality compared to initial stemness. …”
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Integrated transcriptomic and metabolomic analyses reveal heterosis for meat quality of Neijiang pigs by Haifeng Dan, Haifeng Dan, Haifeng Dan, Chengming Liu, Chengming Liu, Chengming Liu, Huiling Zhang, Huiling Zhang, Huiling Zhang, Mailin Gan, Mailin Gan, Mailin Gan, Yan Wang, Yan Wang, Yan Wang, Lei Chen, Lei Chen, Lei Chen, Ye Zhao, Ye Zhao, Ye Zhao, Bin Liu, Kangping Zhu, Lili Niu, Lili Niu, Lili Niu, Li Zhu, Li Zhu, Li Zhu, Linyuan Shen, Linyuan Shen, Linyuan Shen

“…Obese pig breeds have excellent meat quality, while lean pig breeds have high lean meat percentage and feed conversion rate. …”
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Transcriptomic insights into the synergistic effects of darkness and mechanical stimulation on peanut pod development by Lu Huang, Muhammad J. Umer, Hao Liu, Haifen Li, Runfeng Wang, Qianxia Yu, Shaoxiong Li, Rajeev K. Varshney, Manish K. Pandey, Yanbin Hong, Qing Lu, Xiaoping Chen

“…These findings lay a foundation for exploring optimized growth conditions for peanut cultivation, while the identified key genes may serve as potential targets in future peanut breeding programs.…”
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Bile acid synthesis, modulation, and dementia: A metabolomic, transcriptomic, and pharmacoepidemiologic study. by Vijay R Varma, Youjin Wang, Yang An, Sudhir Varma, Murat Bilgel, Jimit Doshi, Cristina Legido-Quigley, João C Delgado, Anup M Oommen, Jackson A Roberts, Dean F Wong, Christos Davatzikos, Susan M Resnick, Juan C Troncoso, Olga Pletnikova, Richard O'Brien, Eelko Hak, Brenda N Baak, Ruth Pfeiffer, Priyanka Baloni, Siamak Mohmoudiandehkordi, Kwangsik Nho, Rima Kaddurah-Daouk, David A Bennett, Shahinaz M Gadalla, Madhav Thambisetty

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Transcriptional landscape of pleural mesothelioma patients in relation to NF2 gene mutational status by Carlos Orozco-Castaño, Alejandro Mejía-Garcia, Hsuan Megan Tsao, Diego A. Bonilla, Carlos Carvajal-Fierro, Ricardo Bruges-Maya, Alba Combita, Rafael Parra-Medina

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