Transcriptomics resources of human tissues and organs by Mathias Uhlén, Björn M Hallström, Cecilia Lindskog, Adil Mardinoglu, Fredrik Pontén, Jens Nielsen

“…Here, we review publicly available human transcriptome resources and discuss body‐wide data from independent genome‐wide transcriptome analyses of different tissues. …”
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APPLICATIONS OF TRANSCRIPTOMICS METHODS IN BREAST CANCER by Yeşim Gökmen Polar

“…The integrated genomic/transcriptomic analysis of breast tumors (METABRIC) and the Cancer Genome Atlas (TCGA) with clinical follow-up data shaped the molecular landscape of breast cancer the last decade. …”
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Transcriptomics data for muscle development in Goats by Yu Pei, Rongsheng Xi, Wenmeng Jiang, Peng Huang, Mei Liu

“…These findings substantially enhance the goat full-length transcriptome database and provide crucial data for uncovering functional genes, epigenetic regulation, and early nutritional intervention strategies relevant to goat meat quality. …”
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Transcriptome Analysis of the Seed Shattering Mechanism in <i>Psathyrostachys juncea</i> Using Full-Length Transcriptome Sequencing by Yuru Lv, Lan Yun, Xiaodi Jia, Yixin Mu, Zhen Li

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Current status of transcriptome sequencing technology in ruminants by Cui JiaYu, Song Lili, Wang Dawei, Liu ZhiLin, Zhang Xin, Jia Zelin, Zhang Yuhang, Xiong Huisheng, Wang Xueli

“…This paper reviews the current status of transcriptome sequencing and the application of transcriptome sequencing technology in ruminants, with a view to providing theoretical reference and basis for the better application of transcriptome sequencing technology in ruminant research.…”
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Topology-aware pathway analysis of spatial transcriptomics by Siras Hakobyan, Maria Schmidt, Hans Binder, Arsen Arakelyan

“…Spatial transcriptomics (ST) has transformed genomics by mapping gene expression onto intact tissue architecture, uncovering intricate cellular interactions that bulk and single-cell RNA sequencing often overlook. …”
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GeneSurfer enables transcriptome-wide exploration and annotation of gene co-expression modules in 3D spatial transcriptomics data by Chang Li, Julian Thijssen, Thomas Kroes, Ximaine van der Burg, Louise van der Weerd, Thomas Höllt, Boudewijn Lelieveldt

“…Demonstrating its utility with both spatially resolved transcriptomics and single-cell RNA sequencing data from the Allen Brain Cell Atlas, GeneSurfer effectively identifies and annotates localized transcriptome-wide co-expression, providing biological insights and facilitating hypothesis generation and validation.…”
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Single-cell transcriptomics in thyroid eye disease by Sofia Ahsanuddin, Albert Y. Wu

“…This timely review summarizes recent breakthroughs and emerging opportunities for using single-cell and single-nuclei transcriptomic data to characterize this highly complex disease state. …”
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Single-cell and spatial transcriptomics in endocrine research by Ryusaku Matsumoto, Takuya Yamamoto

“…Over the past decade, emerging technologies such as single-cell and spatial transcriptomics have provided excellent tools for studying cellular heterogeneity and their interactions; however, the application of these technologies in endocrine research remains limited. …”
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Blood transcriptomic associations of epigenetic age in adolescents by Dennis Khodasevich, Anne K Bozack, Saher Daredia, Julianna Deardorff, Kim G Harley, Brenda Eskenazi, Weihong Guo, Nina Holland, Andres Cardenas

“…Thirteen widely used epigenetic clocks were calculated, and their associations with transcriptome-wide RNA expression were tested using the limma-voom pipeline. …”
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Application of Spatial Transcriptomics in Digestive System Tumors by Bowen Huang, Yingjia Chen, Shuqiang Yuan

“…These technologies are also instrumental in the diagnosis, prognosis, and treatment of digestive system tumors. This review provides a concise introduction to spatial transcriptomics and summarizes recent advances, application prospects, and technical challenges of these technologies in digestive system tumor research. …”
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Dynamic transcriptome landscape of oat grain development by Ting Wang, Bing Han

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Single-cell transcriptomic characterization of microscopic colitis by Stefan Halvorsen, Molly Thomas, Mari Mino-Kenudson, Yuko Kinowaki, Kristin E. Burke, David Morgan, Kaia C. Miller, Katherine M. Williams, Jenny Gurung, Jessica McGoldrick, Megan Hopton, Brooke Hoppe, Nandini Samanta, Sidney Martin, Alice Tirard, Benjamin Y. Arnold, Jessica Tantivit, Joseph Yarze, Kyle Staller, Daniel C. Chung, Alexandra-Chloé Villani, Slim Sassi, Hamed Khalili

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Metabolomic and transcriptomic stress response of Escherichia coli by Szymon Jozefczuk, Sebastian Klie, Gareth Catchpole, Jedrzej Szymanski, Alvaro Cuadros‐Inostroza, Dirk Steinhauser, Joachim Selbig, Lothar Willmitzer

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Interaction between the liver transcriptome and gut microbiota in mice during Toxoplasma gondii infection as identified by integrated transcriptomic and microbiome analysis by Yang Zou, He Ma, Xing Yang, Xin-Yu Wei, Chao Chen, Jing Jiang, Tao Jiang

“…Although T. gondii infection is known to adversely affect the liver and gut microbiota, the precise interplay between the gut microbiome and the liver transcriptome in infected mice remains largely unknown. …”
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Full-length transcriptomes of 25 grassland plant species by Chongyi Jiang, Zixia Huang, Cynthia Meizoso, Gaby Kumpfmüller, Jochen B. W. Wolf, Holger Schielzeth

“…Abstract Grasslands are essential, biodiverse ecosystems providing critical ecosystem services. Despite their ecological and economic value, transcriptomic resources for wild grassland species to support eco-evolutionary and functional genomic studies remain limited. …”
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Transcriptome-wide assessment of human brain and lymphocyte senescence. by Mun-Gwan Hong, Amanda J Myers, Patrik K E Magnusson, Jonathan A Prince

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Cancer staging diagnosis based on transcriptomics and variational autoencoder by LI Jiarui, QIAN Li, SHEN Junjie

“…Objective‍　‍To conduct an in-depth analysis and feature extraction of the transcriptomics data of 10 types of cancers in order to realize the staging diagnosis of cancer samples. …”
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Intracellular spatial transcriptomic analysis toolkit (InSTAnT) by Anurendra Kumar, Alex W. Schrader, Bhavay Aggarwal, Ali Ebrahimpour Boroojeny, Marisa Asadian, JuYeon Lee, You Jin Song, Sihai Dave Zhao, Hee-Sun Han, Saurabh Sinha

“…We present Intracellular Spatial Transcriptomic Analysis Toolkit (InSTAnT), a computational toolkit for extracting molecular relationships from spatial transcriptomics data at single molecule resolution. …”
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Transcriptome analysis of calcium hydroxide tolerance in Enterococcus faecalis by Zhibo Xu, Zhibo Xu, Haonan Ma, Xinmiao Jiang, Quzhen Baima, Yuqi Zhen, Shipeng Yang, Xiuping Meng

“…RNA sequencing further revealed that this tolerance involves multiple interconnected signaling pathways, providing a critical foundation for future research into therapeutic strategies for E. faecalis infections.…”
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