New insights into the transcriptomic profile during the late stages of chicken embryonic development by Di Zhao, Yifan Shi, Jiatai Deng, Bolin Zhong, Yuanyuan Zeng, Qingyuan Ouyang, Haihan Zhang, Zehe Song, Xi He

“…These ceRNA networks provide novel insights and a valuable framework for investigating the molecular regulation of embryonic muscle development in AA broilers and TY chickens.…”
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Salt Stress Leads to Morphological and Transcriptional Changes in Roots of Pumpkins (<i>Cucurbita</i> spp.) by Hongjiu Liu, Ding Ding, Yeshuo Sun, Ruiping Ma, Xiaoqing Yang, Jie Liu, Guoxin Zhang

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Characterizing age-related features for assessing biological age and characteristics in Xinjiang Brown cattle by Jiahao Wang, Menghua Zhang, Qingyao Zhao, Siqian Chen, Yongjie Tang, Quanzhen Chen, Lei Xu, Dan Wang, Xiaoping Guo, Kai Xing, Yachun Wang, ChuduanWang, Xixia Huang, Ying Yu

“…Linear genes were selected using elastic network regression to construct a transcriptomic clock and estimate the biological age of each sample. …”
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Genomic and Transcriptomic Analysis to Explore the Biological Characteristics of <i>Cyclocybe chaxingu</i> by Qiang Yang, Haiyan Song, Ge Su, Xuncheng Wang, Haijing Hu, Zhijun Zhai, Minghui Chen, Jianping Zhou, Hua Yin, Yang Gao, Dianming Hu

“…Transcriptomic analysis revealed distinct gene expression patterns in mycelia, stipe, and cap, reflecting their functional specialization. …”
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SpaMask: Dual masking graph autoencoder with contrastive learning for spatial transcriptomics. by Wenwen Min, Donghai Fang, Jinyu Chen, Shihua Zhang

“…Recent advancements in spatial resolved transcriptomics (SRT) have enabled the analysis of gene expression while preserving the spatial context within tissues. …”
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SCNT: an R package for data analysis and visualization of single-cell and spatial transcriptomics by Jianbo Qing, Jialu Wu, Yafeng Li, Junnan Wu

“…The SCNT (Single-Cell, Single-Nucleus, and Spatial Transcriptomics Analysis and Visualization Tools) package was developed to address these challenges by providing an efficient and user-friendly tool for processing, analyzing, and visualizing SC and ST data. …”
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Transcriptomic HEPN1 signatures predict treatment response in low grade glioma by Lei Jiao, Shuhua Fang, Jianbo Zhang

“…Conclusion The system elucidates the mechanism of iron death related genes in glioma heterogeneity, providing an important theoretical basis for precise treatment of gliomas.…”
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Transcriptomic and Lipidomic Characteristics of Subcutaneous Fat Deposition in Small-Sized Meat Ducks by Hao Zheng, Cui Wang, Ao Zhou, Xing Chen

“…Furthermore, the transcriptomic analysis identified 265 differentially expressed genes (DEGs), including 119 down-regulated and 146 up-regulated genes. …”
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Transcriptome analysis of heterografting on key medicinal compounds accumulation in Ziziphi Spinosae Semen by Xiangrui Fu, Yinfeng Yu, Zikang Lu, Chaohui Wang, Lanping Guo, Yuping Yan, Donglai Ma, Xian Gu

“…Conclusions This study enhances understanding of the molecular mechanisms underlying the effects of heterografting on ZSS quality, providing significant implications for the cultivation and improvement of the quality of medicinal ZSS.…”
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Single-cell transcriptomes reveal spatiotemporal heat stress response in maize roots by Ting Wang, Fanhua Wang, Shuhan Deng, Kailai Wang, Dan Feng, Fan Xu, Weijun Guo, Jia Yu, Yue Wu, Hada Wuriyanghan, Shang-Tong Li, Xiaofeng Gu, Liang Le, Li Pu

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Recent Advances in Transcriptome Analysis Within the Realm of Low Arsenic Rice Breeding by Guanrong Huang, Guoping Yu, Huijuan Li, Haipeng Yu, Zengying Huang, Lu Tang, Pengfei Yang, Zhengzheng Zhong, Guocheng Hu, Peng Zhang, Hanhua Tong

“…Finally, the challenges associated with applying transcriptome analysis to low-As breeding are deliberated upon, and future research directions are envisioned, with the aim of providing references to expedite high-yield and low-arsenic breeding in rice.…”
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Proteomics and transcriptomics combined reveal specific immunological markers in autoimmune thyroid disease by Xia Chen, Hui Chen

“…This study employs a combination of proteomics and transcriptomics analysis to identify and validate specific immune response markers in patients with hyperthyroidism and hypothyroidism, thereby providing a scientific basis for the clinical diagnosis and treatment of AITD.MethodsBy collecting serum and whole blood tissue samples from patients with hyperthyroidism, hypothyroidism, and healthy controls, this study utilizes a combination of transcriptomics and proteomics to analyze changes in immune-related signaling molecules in patients. …”
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Cross-species transcriptome-wide meta-analysis of anterior cruciate ligament rupture by Livia Beccacece, Stefano Pallotti, Yiyun Li, Jie Huang, Leonardo Pasotti, Valerio Napolioni

“…This study aims to identify cross-species responses to ACL rupture providing insights on its molecular basis. We analyzed five publicly available transcriptomic datasets from Homo sapiens, Mus musculus, Canis lupus familiaris, and Oryctolagus cuniculus. …”
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Unraveling the transcriptomic effects of leucine supplementation on muscle growth and performance in basketball athletes. by Sinan Wang, Weishuai Guo, Rui Dong

“…WGCNA highlighted a key module associated with muscle growth, enriched in cytoskeletal pathways. qPCR validation confirmed the upregulation of cytoskeleton-related genes, supporting the transcriptomic findings. These results suggest that leucine enhances muscle adaptation by regulating cytoskeletal dynamics, providing molecular insights into its role in improving athletic performance.…”
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Preweaning heat stress alters liver transcriptome and DNA methylation in dairy calves by Jimena Laporta, Bethany Dado-Senn, Anne R. Guadagnin, Lihe Liu, Francisco Peñagaricano

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Integrated analysis of chromatin and transcriptomic profiling of the striatum after cerebral hypoperfusion in mice by Shijia Le, Fengyiyang Xu, Zhi Luo, Weihao Shi, Shuangshuang Lu, Zengyu Zhang, Zimin Guo, Wenshi Xu, Mingqi Yang, Tianyi Li, Xu Li, Kun Liang, Lei Zhu

“…In parallel, ATAC-seq was used to assess changes in chromatin accessibility within the striatum, providing insight into the epigenome and potential regulatory mechanisms. …”
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Construction of Coexpression Networks Affecting Litter Size in Goats Based on Transcriptome Analysis by Yifan Ren, Junmin He, Guifen Liu, Chen Wei, Xue Li, Jingyi Mao, Guoping Zhang, Wenhao Zhang, Li Long, Ming Wang, Kechuan Tian, Xixia Huang

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TIRE-seq simplifies transcriptomics via integrated RNA capture and library preparation by Piper O’Keeffe, Yasmin Nouri, Hui Shi Saw, Zachery Moore, Tracey M. Baldwin, Sam W. Z. Olechnowicz, Jafar S. Jabbari, David McG Squire, Stephen Leslie, Changqing Wang, Yupei You, Matthew E. Ritchie, Ryan S. Cross, Misty R. Jenkins, Cindy Audiger, Shalin H. Naik, James R. Whittle, Saskia Freytag, Sarah A. Best, Peter F. Hickey, Daniela Amann-Zalcenstein, Rory Bowden, Daniel V. Brown

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Spatiotemporal transcriptome and metabolome landscapes of cotton fiber during initiation and early development by Xuwu Sun, Aizhi Qin, Xingxing Wang, Xiaoyang Ge, Zhixin Liu, Chenxi Guo, Xiaole Yu, Xianliang Zhang, Yao Lu, Jincheng Yang, Jiuming He, Yaping Zhou, Yumeng Liu, Mengke Hu, Hao Liu, Zihao Zhao, Guanjing Hu, Wei Li, Xinshan Zang, Shuai Dai, Susu Sun, Lenin Yong-Villalobos, Luis Herrera-Estrella, Lam-Son Phan Tran, Xiongfeng Ma

“…In this study, we profile the dynamics of transcriptome and metabolome during the early stages of cotton fiber cell development using a combination of spatial transcriptomic, single-cell transcriptomic, and spatial metabolomic analyses. …”
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Transcriptomics, single-cell sequencing and spatial sequencing-based studies of cerebral ischemia by Jiaming Liu, Tao Qing, Mei he, Liu Xu, Zhuxiang Wu, Meiting Huang, Zheyu Liu, Ye Zhang, Zisheng Li, Wenhui Yang, Junbo Liu, Jie Li

“…To comprehensively understand the pathophysiological process of cerebral ischemia and to find new therapeutic strategies, a new approach to cerebral ischemia transcriptomics has emerged in recent years. By integrating data from multiple levels of transcriptomics, such as transcriptomics, single-cell transcriptomics, and spatial transcriptomics, this new approach can provide powerful help in revealing the molecular mechanisms of cerebral ischemia occurrence and development. …”
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