An integrative analysis of cell-specific transcriptomics and nuclear proteomics of sleep-deprived mouse cerebral cortex by Pawan K. Jha, Utham K. Valekunja, Akhilesh B. Reddy

“…Our integrated multi-omics analysis suggests that this distinction arises because neurons and astrocytes employ different gene regulatory strategies under accumulated sleep pressure. …”
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Construction of a prostate adenocarcinoma molecular classification: integrating spatial transcriptomics with retrospective cohort validation by Bingnan Lu, Yifan Liu, Guo Ji, Yuntao Yao, Zhao Yang, Bolin Zhu, Lei Wang, Keqin Dong, Yuanan Li, Jiaying Shi, Junzhe He, Runzhi Huang, Wang Zhou, Xinming Cui, Xiuwu Pan, Xingang Cui

“…Methods Through spatial transcriptome analysis, we identified different malignant cell/spot types in PRAD. …”
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Disparate and shared transcriptomic signatures associated with cortical atrophy in genetic behavioral variant frontotemporal degeneration by Ting Shen, Jacob W. Vogel, Vivianna M. Van Deerlin, EunRan Suh, Laynie Dratch, Jeffrey S. Phillips, Lauren Massimo, Edward B. Lee, David J. Irwin, Corey T. McMillan

“…MAPT-bvFTD displayed more pronounced differences in transcriptomic signatures compared to the other two genetic forms. …”
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Transcriptomic response of the picoalga Pelagomonas calceolata to nitrogen availability: new insights into cyanate lyase function by Nina Guérin, Chloé Seyman, Céline Orvain, Laurie Bertrand, Priscillia Gourvil, Ian Probert, Benoit Vacherie, Élodie Brun, Ghislaine Magdelenat, Karine Labadie, Patrick Wincker, Adrien Thurotte, Quentin Carradec

“…Here, we studied the nitrogen metabolism in the cosmopolitan open-ocean picoalga Pelagomonas calceolata (Pelagophyceae and Stramenopiles) in environmental metatranscriptomes and transcriptomes from culture experiments under different nitrogen sources and concentrations. …”
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De novo transcriptome assembly and analysis of differential gene expression in response to drought in European beech. by Markus Müller, Sarah Seifert, Torben Lübbe, Christoph Leuschner, Reiner Finkeldey

“…Gene expression was specific to the different time points, and only five genes were significantly differentially expressed between the stress and control group on all five sampling days. …”
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Time matters: Transcriptomic insights into temporally regulated reproductive and physiological processes in the life cycle of salps. by Svenja J Müller, Ilenia Urso, Sara Driscoll, Katharina Michael, Gabriele Sales, Cristiano de Pittà, Wiebke Wessels, Bettina Meyer

“…Therefore, we generated a de novo transcriptome of Salpa fusiformis to further investigate the physiological processes involved in the life cycle of salps. …”
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De novo assembly of transcriptome during regeneration post-arm amputation in the starfish, Asterias amurensis by Mi Jeong Jo, Hye-Jin Go, Jeong Gyu Kim, Gun-Do Kim

“…This research enhances the understanding of A. amurensis regeneration and highlights the need for further transcriptome analysis across different tissues. Data description A. amurensis, a starfish species found in the northwestern Pacific, is known for its strong predatory behavior and impact on marine biodiversity. …”
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Integrated transcriptomics and epigenomics reveal chamber-specific and species-specific characteristics of human and mouse hearts. by Junpeng Gao, Yuxuan Zheng, Lin Li, Minjie Lu, Xiangjian Chen, Yu Wang, Yanna Li, Xiaomeng Liu, Yun Gao, Yunuo Mao, Peng Zhao, Jinan Zhang, Fuchou Tang, Lei Song, Lu Wen, Jizheng Wang

“…Our results showed conserved region-specific patterns in the mammalian heart at transcriptome and DNA methylation level. Adult and fetal human hearts showed distinct features in DNA methylome, chromatin accessibility, and transcriptome. …”
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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

“…<h4>Conclusion</h4>Our study highlights the importance of integrating different modalities of transcriptomic data for a better understanding of the molecular mechanisms. …”
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De novo transcriptome assembly of Acartia tonsa adults using Nanopore long-read sequencing by Florencia Mohamed, Marco Picone, Greta Battaggia, Ilenia Urso, Elisa Camatti, Alessandro Vezzi, Gabriele Sales

“…In this study, we present a de novo transcriptome of A. tonsa adult copepods exposed to different neonicotinoids obtained from Nanopore sequences. …”
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Prognostic Value of Centrosome Replication-Related Genes in Prostate Cancer Based on Transcriptomic and Mendelian Randomization by Qizhong Lu, Yufan Wu, Qiwei Yu, Jun Ouyang

“…In this study, we utilized PCa transcriptome data from public databases and applied bioinformatics methods to identify three prognostic genes ( CDC20 , RAD51 , and TTK ) related to centrosome duplication in PCa. …”
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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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Comparative Transcriptome Analysis of Recessive Male Sterility (RGMS) in Sterile and Fertile Brassica napus Lines. by Cunmin Qu, Fuyou Fu, Miao Liu, Huiyan Zhao, Chuan Liu, Jiana Li, Zhanglin Tang, Xinfu Xu, Xiao Qiu, Rui Wang, Kun Lu

“…However, the complete molecular mechanism of the male sterility during male-gametogenesis in RGMS remains to be determined. To identify transcriptomic changes that occur during the transition to male sterility in RGMS, we examined the male sterile line WSLA and male fertile line WSLB, which are near-isogenic lines (NILs) differing only in the fertility trait. …”
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De Novo transcriptome assembly and annotation of the wild service tree Sorbus torminalis (L.) Crantz by Sara Pinosio, Camilla Avanzi, Francesca Bagnoli, Ilaria Spanu, Giovanni Giuseppe Vendramin, Andrea Piotti

“…This dataset was used to produce and annotate the first transcriptome assembly for S. torminalis, paving the way for future genomic research and applications in this species. …”
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Combined analysis of metabolomics and transcriptomics reveals the effects of sugar treatment on postharvest strawberry fruit quality by Zihui Zhang, Riru Tian, Junyi Wan, Yan Wang, He Li

“…Based on these results, combined metabolomic and transcriptomic analyses were performed to assess the impact of 0.2 mol∙L−1 fructose treatment. …”
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Deciphering the cellular and molecular landscape of cervical cancer progression through single-cell and spatial transcriptomics by Peng Xia, Juanhong Zhou, Rong Shen, Degui Wang

“…This study employed an integrated approach combining single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (stRNA-seq) to comprehensively characterize the tumor microenvironment (TME) across different stages of cervical cancer development. …”
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Genome and transcriptome analysis of the basidiomycetous yeast Pseudozyma antarctica producing extracellular glycolipids, mannosylerythritol lipids. by Tomotake Morita, Hideaki Koike, Hiroko Hagiwara, Emi Ito, Masayuki Machida, Shun Sato, Hiroshi Habe, Dai Kitamoto

“…P. antarctica genome exhibited a remarkable degree of synteny to U. maydis genome, however, the comparison of the gene expression profiles under the culture on the two carbon sources, glucose and soybean oil, by the DNA microarray method revealed that transcriptomes between the two species were significantly different. …”
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Integrated Metabolome and Transcriptome Analyses Provides Insights into Ovule Abortion in <i>Camellia oleifera</i> by Yayan Zhu, Jiajuan Xu, Gang Wang, Feng Xiao, Minggang Zhang, Qinmeng Zeng, Jie Xu

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Gene Fusion Detection in Long-Read Transcriptome Datasets from Multiple Cancer Cell Lines by Keigo Masuda, Yoshiaki Sota, Hideo Matsuda

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Transcriptome Analysis and Sensory Evaluation of Thai Native Chicken Raised in Conventional and Free-Range Conditions by P. Seritrakul, P. Poommarin

“…At 6 months, blood samples were collected for transcriptome analysis and verified by quantitative real-time PCR. …”
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