Whole-blood transcriptome profiling reveals signatures of metformin and its therapeutic response. by Monta Briviba, Laura Ansone, Ivars Silamikelis, Vita Rovite, Ilze Elbere, Laila Silamikele, Ineta Kalnina, Davids Fridmanis, Jelizaveta Sokolovska, Ilze Konrade, Valdis Pirags, Janis Klovins

“…We chose the RNA-Seq-based comparative transcriptomics approach to evaluate the systemic effect of metformin and highlight potential predictive biomarkers of metformin response in drug-naïve volunteers with type 2 diabetes in vivo. …”
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A deep proteome and transcriptome abundance atlas of 29 healthy human tissues by Dongxue Wang, Basak Eraslan, Thomas Wieland, Björn Hallström, Thomas Hopf, Daniel Paul Zolg, Jana Zecha, Anna Asplund, Li‐hua Li, Chen Meng, Martin Frejno, Tobias Schmidt, Karsten Schnatbaum, Mathias Wilhelm, Frederik Ponten, Mathias Uhlen, Julien Gagneur, Hannes Hahne, Bernhard Kuster

“…Abstract Genome‐, transcriptome‐ and proteome‐wide measurements provide insights into how biological systems are regulated. …”
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Deep Learning-Enabled Integration of Histology and Transcriptomics for Tissue Spatial Profile Analysis by Yongxin Ge, Jiake Leng, Ziyang Tang, Kanran Wang, Kaicheng U, Sophia Meixuan Zhang, Sen Han, Yiyan Zhang, Jinxi Xiang, Sen Yang, Xiang Liu, Yi Song, Xiyue Wang, Yuchen Li, Junhan Zhao

“…This enhancement enables more accurate gene expression analysis and aids in identifying prognostic marker genes, outperforming state-of-the-art deep learning methods with a total improvement of up to 49.72%. GIST provides a generalizable framework for integrating histology with spatial transcriptome analysis, revealing novel insights into spatial organization and functional dynamics.…”
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Transcriptomic landscape of Hras12V oncogene-induced hepatocarcinogenesis with gender disparity by Huaiyuan Di, Zhuona Rong, Nan Mao, Huiling Li, Jun Chen, Renwu Liu, Aiguo Wang

“…Abstract The genesis of hepatocellular carcinoma (HCC) is closely related to male factors and hyper-activated Ras signals. A transcriptomic database was established via RNA-Seq of HCC (T) and the adjacent precancerous liver tissue (P) of Hras12V transgenic mice (Ras-Tg, HCC model) and the normal liver tissue of wild-type mice (W) of both sexes. …”
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Transcriptomic analysis of bone transport reveals different functions between both ends by Maochun Wang, Jiao Zhang, Chongxu Qiao, Shunchao Yan, Weicheng Gao, Guoping Wu

“…Notably, 15 DEGs were shared between the TE and CE groups, with consistent expression trends, suggesting partially overlapping molecular mechanisms in bone healing under different mechanical ends.ConclusionThese findings provided insights into the distinct and shared molecular pathways involved in bone regeneration during bone transport and could inform targeted therapeutic strategies to enhance bone healing.…”
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Insights into the molecular mechanisms of browning tolerance in luffa: a transcriptome and metabolome analysis by Shan Wu, Miao Sun, Huashan Lian

“…These findings provide a theoretical foundation for further investigation into the molecular mechanisms underlying luffa browning and offer potential targets for genetic improvement or breeding strategies to enhance luffa quality.…”
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Characteristics of transcriptome and chromatin accessibility in the peripheral blood after acute hypoxia exposure by Kuo Zeng, Pei-ru Yuan, Jin-feng Xuan, Lai-xi Zhao, Xiao-na Li, Jun Yao, Dong Zhao

“…Conclusions Our results can provide the reference for the early response of the organism to hypoxic adaptation.…”
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Spatial transcriptomics reveals regionally altered gene expression that drives retinal degeneration by Ulrike Schumann, Lixinyu Liu, Riemke Aggio-Bruce, Adrian V. Cioanca, Artur Shariev, Michele C. Madigan, Krisztina Valter, Jiayu Wen, Riccardo Natoli

“…We identify regionally distinct transcriptomes, with higher expression of immunity related genes in the superior retina. …”
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Transcriptome analysis unveils survival strategies of Streptococcus parauberis against fish serum. by Yoonhang Lee, Nameun Kim, HyeongJin Roh, Ahran Kim, Hyun-Ja Han, Miyoung Cho, Do-Hyung Kim

“…These results indicate that S. paraubers can resist and evade the humoral immune responses of fish. The transcriptomic data obtained in this study provide a better understanding of the mode of action of S. parauberis in fish.…”
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Transcriptomic Analysis Reveals the Biosynthesis Mechanism of Coixol Under Salicylic Acid Treatment by Yao Wang, Hanli Ye, Xuqin Luo, Ziwei Li, Chuanqi Zheng, Dali Sun

“…The biosynthesis pathway of coixol was determined by high-throughput transcriptome sequencing analysis and the genes were then verified by qRT-PCR. …”
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Universal receptive system as a novel regulator of transcriptomic activity of Staphylococcus aureus by George Tetz, Kristina Kardava, Maria Vecherkovskaya, Alireza Khodadadi-Jamayran, Aristotelis Tsirigos, Victor Tetz

“…To this end, transcriptomic analysis of S. aureus MSSA VT209 was performed following the destruction of TezRs. …”
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Inferring causal metabolic signals that regulate the dynamic TORC1‐dependent transcriptome by Ana Paula Oliveira, Sotiris Dimopoulos, Alberto Giovanni Busetto, Stefan Christen, Reinhard Dechant, Laura Falter, Morteza Haghir Chehreghani, Szymon Jozefczuk, Christina Ludwig, Florian Rudroff, Juliane Caroline Schulz, Asier González, Alexandre Soulard, Daniele Stracka, Ruedi Aebersold, Joachim M Buhmann, Michael N Hall, Matthias Peter, Uwe Sauer, Jörg Stelling

“…Our inference method identified putative downstream targets of TORC1 and putative metabolic inputs of TORC1, including the hypothesized glutamine signal. The work provides a basis for further mechanistic studies of nitrogen metabolism and a general computational framework to study cellular processes.…”
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Transcriptome‐wide analysis of circRNA and RBP profiles and their molecular relevance for GBM by Julia Latowska‐Łysiak, Żaneta Zarębska, Marcin P. Sajek, Adriana Grabowska, Alessia Buratin, Paweł Głodowicz, Julia O. Misiorek, Konrad Kuczyński, Stefania Bortoluzzi, Marek Żywicki, Jan G. Kosiński, Agnieszka Rybak‐Wolf, Rafał Piestrzeniewicz, Anna M. Barciszewska, Katarzyna Rolle

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Comparatively profiling the transcriptome of human, Porcine and mouse oocytes undergoing meiotic maturation by Naru Zhou, Xin Wang, Yi Xia, Zongliang Liu, Lei Luo, Rentao Jin, Xianhong Tong, Zhenhu Shi, Zhichao Wang, Heming Sui, Yangyang Ma, Yunsheng Li, Zubing Cao, Yunhai Zhang

“…Results Transcriptome analysis identified 4,625, 3,824, 4,972 differentially expressed genes (DEGs) between the germinal vesicle (GV) and metaphase II (MII) stage in human, porcine and mouse oocytes respectively. …”
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Integrative Transcriptomic and Metabolomic Insights Into Saline-Alkali Stress Tolerance in Foxtail Millet by Mengxia Han, Qing Tan, Yulu Yang, Hui Zhang, Xingchun Wang, Xukai Li

“…This study examined the transcriptomic and metabolomic responses of two contrasting foxtail millet varieties, B103 (tolerant) and B323 (sensitive), under saline-alkali stress. …”
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Transcriptome Analysis Reveals the Requirement of the TGFβ Pathway in Ascidian Tail Regression by Wenjie Shi, Penghui Liu, Dongyu Yang, Yuan Zhuang, Boyan Lin, Bo Dong

“…We further investigated the downstream gene network of the TGFβ signaling pathway through comparative transcriptome data analysis on the TGFβ pathway inhibition samples. …”
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Comparative Transcriptome Analysis in Eggplant Reveals Selection Trends during Eggplant Domestication by Qingzhen Wei, Liming Du, Wuhong Wang, Tianhua Hu, Haijiao Hu, Jinglei Wang, Karine David, Chonglai Bao

“…Taken together, our results shed light on the effects of artificial and natural selection on the transcriptomes of eggplant and its wild relatives. Identification of the selected genes will facilitate the understanding of genetic architecture of domesticated-related traits and provide resources for resistant breeding in eggplant.…”
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Whole-Transcriptome Analysis Reveals the Regulatory Network of Immune Response in Dapulian Pig by Tao Wang, Zhe Tian, Mubin Yu, Shuer Zhang, Min Zhang, Xiangwei Zhai, Wei Shen, Junjie Wang

“…Generally, the immune response is an important part of anti-disease capability; however, the related mechanism in pigs is largely puzzling. Here, the public transcriptome data of peripheral blood mononuclear cells (PBMCs) from Dapulian (Chinese local breed) and Landrace (Commercial breed) pigs after stimulation with polyinosinic-polycytidylic acid (poly I:C, a conventional reagent used for simulation of the viral infection) were reanalyzed, and the immune response mechanism in different pig breeds was investigated from a transcriptomic perspective. …”
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Transcriptome Differential Expression Regulation Analysis of the Narrow-Leaf Mutant of Sorghum Bicolor by Jinhong Li, Yiwei Wang, Yuche Zhao, Shirui Zhang, Chunyu Wang, Ling Cong, Yanpeng Zhang, Shuang Gang, Xiaochun Lu

“…These genes are differentially expressed in nal6, directly affecting the signaling of auxin and zeatin and the biosynthesis of zeatin. Our findings provide a theoretical foundation for understanding the molecular regulation of narrow leaves and breeding ideal plant types in <i>Sorghum bicolor</i>.…”
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De novo transcriptome assembly and annotation of the semi-wild Gayal (Bos frontalis) by Zhendong Gao, Bo Wang, Ying Lu, Yuqing Chong, Mengfei Li, Jieyun Hong, Jiao Wu, Dongmei Xi, Weidong Deng

“…Additionally, long non-coding RNAs (lncRNAs) were identified across all sampled tissues, and comprehensive gene expression profiles and differential expression gene analyses were performed. These findings provide a rich repository of genetic information, laying the foundation for comprehensive functional genomics studies and paving the way for deeper insights into the molecular mechanisms of the Gayal, thereby advancing our understanding of its transcriptome architecture and offering crucial data for conservation efforts and practical applications.…”
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