Unraveling calcium dysregulation and autoimmunity in immune mediated rippling muscle disease by Samir R. Nath, Aneesha Dasgupta, Divyanshu Dubey, Eileen Kokesh, Grayson Beecher, Numrah Fadra, Teerin Liewluck, Sean Pittock, Jason D. Doles, William Litchy, Margherita Milone

“…This study represents the first muscle transcriptomic analysis of iRMD patients and dissects underlying disease mechanisms. …”
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Integrated mRNA and miRNA Analysis Reveals Layer-Specific Mechanisms of Antler Yield Variation in Sika Deer by Derui Zhao, Zhen Zhang, Qianghui Wang, Heping Li

“…This study aimed to elucidate the transcriptomic and post-transcriptional mechanisms underlying antler yield variation by comparing gene and miRNA expression profiles across four distinct antler tissue layers—dermis (D), reserve mesenchyme (RM), pre-cartilage (PC), and cartilage (C)—in sika deer with different yields. …”
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Catabolism Mechanism and Growth-Promoting Effect of Xylooligosaccharides in <i>Lactiplantibacillus plantarum</i> Strain B20 by Yini Shi, Huan Wang, Zhongke Sun, Zifu Ni, Chengwei Li

“…Using the <i>Lb. plantarum</i> strain SK151 genome as a reference, bioinformatic analysis failed to identify any previously characterized genes responsible for the uptake and catabolism of XOS. However, transcriptomic analysis of <i>Lb. plantarum</i> B20 yielded numerous differentially expressed genes (DEGs) during fermentation of XOS. …”
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Response to Oxidative Stress Induced by Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine in Differentiated PC12 Cells by Cunzhi Li, Xiaoqiang Lv, Zhiyong Liu, Hui Deng, Ting Gao, Huan Li, Xinying Peng, Airong Qian, Junhong Gao, Lifang Hu

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Exploring the regulatory mechanisms of reproductive dysfunction in obese patients with PCOS by Jing Cui, Hui Chang, Yunxia Song, Haiyan Wang, Lin Sun

“…This study aims to uncover the molecular mechanisms underlying reproductive dysfunction in obese PCOS patients by identifying key regulatory genes, pathways, and immune interactions, with a focus on cross-tissue regulators and potential therapeutic targets. We analyzed transcriptomic data from multiple datasets, including GSE43322, GSE43264, GSE124226, GSE54250, GSE48301, and GSE114419. …”
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Elucidating the Mechanism of Temporal Adaptation to Hydrogen Peroxide‐Induced Oxidative Stress in Corynebacterium glutamicum by Chang Yu, Wenjing Hu, Xiaoyu Li, Yu Lei, Dandan Gao, Meng Wang, Ping Zheng, Yan Zhu, Jibin Sun

“…Overall, this study provides the most comprehensive analysis to date of temporal cellular adaptation to H2O2 stress in C. glutamicum, establishing a foundation for future applications in both biomanufacturing and antimicrobial research.…”
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Spatiotemporal single-cell analysis elucidates the cellular and molecular dynamics of human cornea aging by Dan Jiang, Ke Li, Yining Sun, Zicheng Zhang, Shuang Xie, Xintong Yu, Ruoqi Wang, Ying Feng, Qinxiang Zheng, Yajing Wen, Peter S. Reinach, Yuanyuan Du, Meng Zhou, Wei Chen

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Identification of functional pathways and hub genes associated with the heterochronic development of sugarcane axillary buds and sett roots through multi-omics analysis by Jiabao Zheng, Xiaoyu Huang, Yanli Wei, Wenyan Li, Baoshan Chen, Baoshan Chen, Wenlan Li, Wenlan Li

“…In addition, we identified differentially expressed genes through transcriptomic analysis and discovered, via GO and KEGG enrichment analyses, that negative regulation of external stimulus response is a key to the preference of ZZ2 for early bud sprouting. …”
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Spatial gene expression profiling identifies prognostic features of residual tumors after neoadjuvant chemotherapy in triple-negative breast cancer by Hye Sung Won, Yong-Seok Kim, Kyung Jin Seo, Sun-Young Jun, Der Sheng Sun, Mihong Choi, Jung-Sook Yoon, Jae Ho Byun

“…We investigated genetic alterations related to recurrence using spatial transcriptomic analyses of residual tumors from patients who had and had not relapsed after NAC for early-stage TNBC.MethodsThirteen patients who underwent curative resection after NAC for early-stage TNBC, six of whom experienced recurrence, were included. …”
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Metabolic, transcriptional, and hormonal responses of Panax ginseng C. A. Meyer to nitrogen deficiency by Hao Liang, Hai Sun, Cai Shao, Bochen Lv, Jiapeng Zhu, Weiyu Cao, Jixin Zhou, Yayu Zhang

“…However, an integrated analysis of the metabolome, transcriptome, and hormone profiles associated with N deficiency in Panax ginseng has not been previously conducted. …”
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Allelopathic Molecular Mechanisms of the Two Main Allelochemicals in Sweet Potato by Ruiguo Shi, Guimei Jin, Shicai Shen, Gaofeng Xu, Fengping Zheng, David Roy Clements, Yunhai Yang, Shaosong Yang, Fanghao Wan, Fudou Zhang, Bo Liu

“…Therefore, metabolomic and transcriptomic analyses were performed to explore the allelopathic effects, metabolic pathway, and associated genes for two major compounds with allelopathic activity, palmitic acid and linoleic acid. …”
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Global changes in gene expression of mRNA and miRNA in liver tissues of Micropterus salmoides after infection with Aeromonas hydrophila by Zhi Lei Yao, Ming Yu, Xiao Wang, Hong Ju Chen, Xiang Shan Ji, Yan Zhao

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LncRNA transcriptome analysis of rainbow trout (Oncorhynchus mykiss) skin infected with IHNV reveals that lncRNA SARL/miR-205-z/SOCS3 axis negatively regulates antiviral immunity m... by Lu Zhao, Jinqiang Huang, Yongjuan Li, Shenji Wu

“…Furthermore, SOCS3 overexpression significantly promoted the replication of IHNV. This study provides fundamental data for disease resistance breeding and targeted drug therapy in rainbow trout.…”
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Short-Term Fertilization with the Nitrogen-Fixing Bacterium (NFB) <i>Kosakonia radicincitans</i> GXGL-4A Agent Can Modify the Transcriptome Expression Profiling of Cucumber (<i>Cuc... by Baoyun Feng, Erxing Wang, Yating Zhang, Lurong Xu, Yanwen Xue, Yunpeng Chen

“…This study contributes to a deeper understanding of the interaction between NFB and plants and provides theoretical guidance for the development of GXGL-4A as a mature biological agent for sustainable agricultural production under drought stress.…”
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Mining Key Drought-Resistant Genes of Upland Cotton Based on RNA-Seq and WGCNA Analysis by Hu Zhang, Wen Zhang, Yu Tang, Yuantao Guo, Jinsheng Wang, Wenju Gao, Qingtao Zeng, Quanjia Chen, Qin Chen

“…This study reveals, for the first time, the possible dual regulatory mechanism of WRKY22 in cotton’s drought resistance, providing a theoretical basis for cotton drought-resistant breeding.…”
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A panoramic view of cotton resistance to Verticillium dahliae: From genetic architectures to precision genomic selection by Xiaojun Zhang, Shiming Liu, Peng Wu, Wanying Xu, Dingyi Yang, Yuqing Ming, Shenghua Xiao, Weiran Wang, Jun Ma, Xinhui Nie, Zhan Gao, Junyuan Lv, Fei Wu, Zhaoguang Yang, Baoxin Zheng, Ping Du, Jiangmei Wang, Hao Ding, Jie Kong, Alifu Aierxi, Yu Yu, Wei Gao, Zhongxu Lin, Chunyuan You, Keith Lindsey, Nataša Štajner, Maojun Wang, Jiahe Wu, Shuangxia Jin, Xianlong Zhang, Longfu Zhu

“…Here, we unraveled the genetic architectures and regulatory landscape of VW resistance in cotton by combining genome‐wide association studies (GWAS) and transcriptome‐wide association studies (TWAS) using 1152 transcriptomes derived from 290 cotton accessions. …”
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A companion to the preclinical common data elements for genomics, transcriptomics, and epigenomics data in rodent epilepsy models. A report of the TASK3‐WG4 omics working group of... by Erwin A. vanVliet, Michael S. Hildebrand, James D. Mills, Gary P. Brennan, Tore Eid, Susan A. Masino, Vicky Whittemore, Laura Bindila, Kevin K. Wang, Manisha Patel, Piero Perucca, Christopher A. Reid

“…We discuss the important elements that need to be considered for genomics, transcriptomics, and epigenomics methodologies, providing a rationale for the parameters that should be collected. …”
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Identification of a Highly Virulent <i>Verticillium nonalfalfae</i> Strain Vn011 and Expression Analysis of Its Orphan Genes During Potato Inoculation by Mengyuan Wan, Xinlong Chen, Xiaoxi Yi, Yi Fu, Yuanliang Jin, Dianqiu Lyu

“…Further research on these orphan genes will not only enhance the understanding of the evolutionary adaptation of <i>V. nonalfalfae</i>, but may also provide new molecular targets for the control of potato wilt disease.…”
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Optimized chemical labeling method for isolation of 8-oxoG-modified RNA, ChLoRox-Seq, identifies mRNAs enriched in oxidation and transcriptome-wide distribution biases of oxidation... by Matthew R. Burroughs, Philip J. Sweet, Lydia M. Contreras

“…By applying ChLoRox-Seq to mRNA extracted from human lung epithelial cells (BEAS-2B) after exposure to environmentally relevant stress, we observe that 8-oxoG modifications tend to cluster in regions that are G-rich and within mRNA transcripts possessing longer 5’ UTR and CDS regions. These findings provide new insight into the complex mechanisms that bias the accumulation of RNA oxidation across the transcriptome. …”
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Role of next‐generation sequencing in revolutionizing healthcare for cancer management by Om Saswat Sahoo, Hiya Aidasani, Arnab Nayek, Smita Tripathi, Joyeeta Talukdar, Anamta Gul, Deepak Kumar, Ruby Dhar, Subhradip Karmakar

“…Furthermore, the integration of spatial transcriptomics is highlighted as a frontier in understanding the tumor microenvironment. …”
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