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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GhLPF1 Associated Network Is Involved with Cotton Lint Percentage Regulation Revealed by the Integrative Analysis of Spatial Transcriptome by Hongyu Wu, Luyao Wang, Shengjun Zhao, Mengtao Gao, Junfeng Cao, Yupeng Hao, Li Yu, Ting Zhao, Siyuan Wang, Jin Han, Yumeng Zhu, Yongyan Zhao, Jie Li, Ke Nie, Kening Lu, Linyun Ding, Zhiyuan Zhang, Tianzhen Zhang, Xueying Guan

“…Abstract Cotton fibers, derived from the epidermis of the ovule, provide a sustainable natural fiber source for the textile industry. …”
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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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Integrative analysis of 115 transcriptomic studies decodes the molecular landscape of neurodevelopmental disorders by Jarno Koetsier, Lars M. T. Eijssen, Leon J. Schurgers, Leopold M. G. Curfs, Chris P. Reutelingsperger, Nasim Bahram Sangani

“…Abstract Due to the low disease prevalence, transcriptomic studies of neurodevelopmental disorders (NDDs) often face limited statistical power, constraining the depth of insights they can provide. …”
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Transcriptome sequencing of Codonopsis pilosula and identification of candidate genes involved in polysaccharide biosynthesis. by Jian Ping Gao, Dong Wang, Ling Ya Cao, Hai Feng Sun

“…<h4>Significance</h4>To our knowledge, this is the first study to provide a public transcriptome dataset prepared from C. pilosula and an outline of the biosynthetic pathway of polysaccharides in a medicinal plant. …”
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Combined metabolome and transcriptome analysis reveal the mechanism of water stress in Ophiocordyceps sinensis by Li He, ChuanYong Li, ZhaoHe Chen, YanLi Huo, Bo Zhou, Fang Xie

“…Conclusions Overall, our findings provide important information for further exploration of the mechanism underlying the water stress tolerance of O. sinensis for the industrialization of artificial cultivation of Chinese cordyceps.…”
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Transcriptome profiling and co-expression network analysis of 96 Haematococcus pluvialis samples by Bin Hu, Kai Liu, Feichao Du, Hailiang Xing, Xiaoyuan Su, Tao Hu, Feng Chen, Yujie Qin, Zhaozhen Dong, Xue Sun, Liuquan Zhang, Jagroop Pandhal, Nianjun Xu, Chaoyang Hu

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Decoding hippocampal subfield and glial responses in ischemia using single-cell transcriptomics by Donghee Kwak, Ji Hyun Park, Yun Hak Kim, Hong Il Yoo

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Transcriptomic analysis of maize leaves under different irrigation treatments in field conditions by Yuan-Xin Li, Ru-Zhi Li, Jing Yang, Zhi-Wei Wang, Xiao-Guang Li, Hou-Zhen Yi, Xin-Ping Guo, Hang Zhou, Kai-Hua Jia, Peng-Fei Chu

“…This not only deepens our understanding of maize’s response to water stress but also provides valuable genetic resources and theoretical insights for future genetic improvement. …”
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Comparative phenotypic, physiological, and transcriptomic responses to drought and recovery in two Fraxinus species by Tae-Lim Kim, Hyemin Lim, Kyungmi Lee, Michael Immanuel Jesse Denison, Sathishkumar Natarajan, Changyoung Oh

“…This study aimed to compare the phenotypic, physiological, and transcriptomic characteristics of drought-stressed and recovered rewatered plants in a time-course experiment. …”
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Effects of supplementary light treatment on saffron: integrated physiological, metabolomic, and transcriptome analyses by Li Li, Yujie Zhou, Jingting Wang, Xiwu Qi, Hailing Fang, Yang Bai, Zequn Chen, Xu Yu, Dongmei Liu, Qun Liu, Chengyuan Liang

“…Expression analysis of key genes and their correlations with crocin-related metabolites may provide useful information for screening functional genes involved in crocin synthesis. …”
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spVelo: RNA velocity inference for multi-batch spatial transcriptomics data by Wenxin Long, Tianyu Liu, Lingzhou Xue, Hongyu Zhao

“…Here, we introduce spVelo, a scalable framework for RNA velocity inference of multi-batch spatial transcriptomics data. spVelo supports several downstream applications, including uncertainty quantification, complex trajectory pattern discovery, driver marker identification, gene regulatory network inference, and temporal cell-cell communication inference. spVelo has the potential to provide deeper insights into complex tissue organization and underscore biological mechanisms based on spatially resolved patterns.…”
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Seasonal transcriptomic shifts reveal metabolic flexibility of chemosynthetic symbionts in an upwelling region by Isidora Morel-Letelier, Benedict Yuen, Luis H. Orellana, A. Carlotta Kück, Yolanda E. Camacho-García, Minor Lara, Matthieu Leray, Laetitia G. E. Wilkins

“…These conditions serve as a natural experiment that provides a unique opportunity to study how marine animals and their associated microorganisms respond in the face of environmental change. …”
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Protocol for single-cell RNA sequencing and spatial transcriptomics of bladder Ewing sarcoma by Weipu Mao, Houliang Zhang, Jie Ji, Jianpung Wu, Ming Chen, Chao Sun

“…Spatial transcriptomics, meanwhile, delivers spatial visualization and quantitative analysis of tissue sections. …”
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Analysis of differential gene expression and novel transcript units of ovine muscle transcriptomes. by Chunlan Zhang, Guizhi Wang, Jianmin Wang, Zhibin Ji, Fei Dong, Tianle Chao

“…In this study, we characterized differentially expressed genes (DEGs) between the muscle transcriptomes of Small-tailed Han sheep and Dorper sheep and predicted novel transcript units using high-throughput RNA sequencing technology. …”
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STModule: identifying tissue modules to uncover spatial components and characteristics of transcriptomic landscapes by Ran Wang, Yan Qian, Xiaojing Guo, Fangda Song, Zhiqiang Xiong, Shirong Cai, Xiuwu Bian, Man Hon Wong, Qin Cao, Lixin Cheng, Gang Lu, Kwong Sak Leung

“…STModule uncovers diverse expression signals in transcriptomic landscapes such as cancer, intraepithelial neoplasia, immune infiltration, outcome-related molecular features and various cell types, which facilitate downstream analysis and provide insights into tumor microenvironments, disease mechanisms, treatment development, and histological organization of tissues. …”
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