Transcriptome sequencing reveals the evolutionary histories and gene expression evolution in two related Pagurus species. by Zakea Sultana, Isaac Adeyemi Babarinde, Masafumi Nozawa, Kazuho Ikeo, Akira Asakura, Tomoyuki Nakano

“…To investigate the molecular and gene expression evolution that have followed the divergence of these two species, we performed transcriptome sequencing and de novo transcriptome assembly using cephalothorax (head) and pereopod (leg) of the two species. …”
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Identification of ligand and receptor interactions in CKD and MASH through the integration of single cell and spatial transcriptomics. by Jaime Moreno, Lise Lotte Gluud, Elisabeth D Galsgaard, Henning Hvid, Gianluca Mazzoni, Vivek Das

“…Combining single-cell (scRNAseq) and spatial transcriptomics (ST) could give unprecedented molecular disease understanding at single-cell resolution. …”
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Integrated transcriptomics of multiple sclerosis peripheral blood mononuclear cells explored potential biomarkers for the disease by Arman Mokaram Doust Delkhah

“…However, given that they were downregulated in the integrated data while they were upregulated in the validation sets, they could not be considered as potential biomarkers for the disease. …”
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Integrating metabolomics and transcriptomics comprehensively reveals the global metabolic differences in three species of Nitraria berries by Yanhong Li, Shengyan Wang, Qing Zhao, Qian Wang, Zufan Yang, Qiangqiang Jia

“…This study combined metabolomics and transcriptomics to explore the differences among three species of Nitraria berries. …”
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Comprehensive transcriptome analysis of developing xylem responding to artificial bending and gravitational stimuli in Betula platyphylla. by Chao Wang, Nan Zhang, Caiqiu Gao, Zhiyuan Cui, Dan Sun, Chuanping Yang, Yucheng Wang

“…Our study showed that during TW formation, genes involved in cellulose synthesis were induced, while the expression of lignin synthesis-related genes decreased, resulting in increased cellulose content and decreased lignin levels in TW. …”
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Variational graph autoencoder for reconstructed transcriptomic data associated with NLRP3 mediated pyroptosis in periodontitis by Pradeep K. Yadalam, Prabhu Manickam Natarajan, Carlos M. Ardila

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Clonal phylogenies inferred from bulk, single cell, and spatial transcriptomic analysis of epithelial cancers. by Andrew Erickson, Sandy Figiel, Timothy Rajakumar, Srinivasa Rao, Wencheng Yin, Dimitrios Doultsinos, Anette Magnussen, Reema Singh, Ninu Poulose, Richard J Bryant, Olivier Cussenot, Freddie C Hamdy, Dan Woodcock, Ian G Mills, Alastair D Lamb

“…Finally, a comparison of pseudo-bulked spatial transcriptomic data to adjacent sections with WGS data also demonstrated recapitulation of ground truth (entanglement = 0.35). …”
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Dual RNA-seq reveals transcriptome changes during Fusarium virguliforme-Trichoderma afroharzianum interactions. by Mirian F Pimentel, Leonardo F Rocha, Arjun Subedi, Jason P Bond, Ahmad M Fakhoury

“…Trichoderma spp. are among the most studied biocontrol agents. While extensive work has been done to understand Trichoderma antagonistic mechanisms, additional research is needed to fully understand how Trichoderma spp. recognize the pathogen-host and the intra-species variability i frequently observed upon interaction with a specific pathogen-host. …”
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The spatial transcriptome of the late-stage embryonic and postnatal mouse brain reveals spatiotemporal molecular markers by Yuichiro Hara, Takuma Kumamoto, Naoko Yoshizawa-Sugata, Kumiko Hirai, Xianghe Song, Hideya Kawaji, Chiaki Ohtaka-Maruyama

“…However, markers established in the adult brain sometimes behave differently in the fetal brain, actively changing during development. The spatial transcriptome is a powerful analytical method that enables sequence analysis while retaining spatial information. …”
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Transcriptome reveal gene regulation mechanisms of the barnacle Chthamalus challengeri for microhabitat adaption in the intertidal zone by HaoYuan Li, MengMeng Huang, ZhiBin Gan, XinZheng Li

“…Results In this study, we designed a series of in situ tidal conditions for C. challengeri and sequenced their transcriptome collected from various microhabitats. We aimed to detect the genetic adaptation mechanisms of barnacles responding to the microhabitat changes in the intertidal zone based on comparative transcriptomics. …”
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Methanol fixation and tagmentation of RNA/DNA hybrids directly enable single-cell transcriptome sequencing by Tao Xu, Yicong Xu, Ziyang An, Yiheng Li, Jiawen Yang, Weixing Zhang, Jin Xu

“…However, prevalent methods predominantly employ 3′-end sequencing of transcripts, limiting the analysis of alternative splicing and other post-transcriptional processes. While full-length single-cell transcriptome sequencing methods, such as Smart-seq, offer more comprehensive information, but are restricted by low-throughput. …”
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Transcriptome and Metabolome Analysis Reveals the Effect of Temperature on the Vegetative Mycelium of <i>Morchella sextelata</i> by Xinyu Hu, Leran Ma, Junhe Liu, Tianyuan Zhang, Zhen Wang

“…In this study, we used <i>Morchella sextelata</i> as the research object and employed integrated transcriptomic and metabolomic analyses to evaluate the effects of cultivation temperatures set at 33 °C, 20 °C, and 4 °C on the vegetative mycelium of <i>Morchella</i>. …”
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Optimization of Protoplast Preparation Conditions in <i>Lyophyllum decastes</i> and Transcriptomic Analysis Throughout the Process by Xiaobin Li, Ying Qin, Yufei Kong, Samantha Chandranath Karunarathna, Yunjiang Liang, Jize Xu

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De novo transcriptome assembly and discovery of drought-responsive genes in white spruce (Picea glauca). by Zoé Ribeyre, Claire Depardieu, Julien Prunier, Gervais Pelletier, Geneviève J Parent, John Mackay, Arnaud Droit, Jean Bousquet, Philippe Nolet, Christian Messier

“…In this study, we examined the transcriptome of white spruce (Picea glauca (Moench) Voss) to identify key genes and metabolic pathways involved in the species' response to water stress. …”
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Transcriptomic and metabolomic analyses provide insights into the biosynthesis of chlorogenic acids in Lonicera macranthoides Hand.-Mazz. by Yuan Pan, Xiao Zhao, Xiao-Li Wu, Yu Wang, Jun Tan, Da-Xia Chen

“…The ion abundances of CGAs were most significantly increased, while some of the CGAs derived and Caffeoyl-CoA-derived substances showed the most largely reduced abundances in the closed bud type (Bt) compared to the flowering type (Ft). …”
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Large-scale transcriptome mining enables macrocyclic diversification and improved bioactivity of the stephanotic acid scaffold by Xiaofeng Wang, Khadija Shafiq, Derrick A. Ousley, Desnor N. Chigumba, Dulciana Davis, Kali M. McDonough, Lisa S. Mydy, Jonathan Z. Sexton, Roland D. Kersten

“…Our study expands stephanotic acid-type peptides to grasses, Lowiaceae, mints, pinks, and spurges while demonstrating that large-scale transcriptome mining can broaden the medicinal chemistry toolbox for chemical and biological exploration of eukaryotic RiPP lead structures.…”
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Single-cell transcriptomics reveals metabolic remodeling and functional specialization in the immune microenvironment of bone tumors by Jun Chen, Na Cui, Shao-Hui He, Chun-Yan Xia, Wei-Qing Li

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Transcriptomics Uncovers Pathways Mediating Low-Nitrogen Stress Tolerance in Two Foxtail Millet Varieties by Jirong Wu, Lu Chen, Zhenrong Yang, Juan Lu, Jinwen Yang, Ning Li, Huawei Shi

“…Compared to the control treatment, 823 differentially expressed genes (DEGs) (350 upregulated, 473 downregulated) were identified in the roots of Dahuanggu, while 2427 DEGs (1703 upregulated, 724 downregulated) were detected in Maotigu under LN treatment. …”
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Transcriptome alterations in long-term mining region residents: Insights into immune response and molecular pathways by Ani Stepanyan, Arsen Arakelyan, Jonathan Schug

“…Additionally, the study identified differences in the transcriptome response between male and female MRR. While females exhibited a stronger immune response, males show dysregulation in ion transport and epigenetic modifications. …”
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An organ‐specific transcriptome atlas of Curcuma wenyujin: MicroRNAs, phasiRNAs, and metabolic pathways by Xiaoxia Ma, Yinju Tang, Zedi Feng, Xiu Yin, Yijun Meng, Xiaopu Yin, Tian Xie

“…In this study, integrated omics data analyses enabled us to discover the microRNAs (miRNAs) and the phased small interfering RNAs (phasiRNAs) on a transcriptome‐wide scale. A total of 186 mature miRNAs and 23 precursors were reported. …”
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