Comparative Transcriptome Analysis of Susceptible and Resistant Rutaceae Plants to Huanglongbing by Huihong Liao, Fuping Liu, Xi Wang, Hongming Huang, Qichun Huang, Nina Wang, Chizhang Wei

“…The transcriptome data showed that in the susceptible Ponkan Mandarin, there were 1519 upregulated genes and 700 downregulated genes, while in the resistant Punctate Wampee variety, there were 1611 upregulated genes and 1727 downregulated genes. …”
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In silico and experimental approaches for validating RNA editing events in transcriptomes by Lai Wei

“…As a typical RNA virus, SARS-CoV-2 is subjected to RNA editing in host cells. While some researchers believe that a traditional variant calling pipeline retrieves all true-positive RNA editing events from the transcriptome, others argue that conventional methods identify many false-positive sites. …”
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Immunosuppression of spleen in mice treated with erythropoietin: transcriptomic and immunological analysis by Xinyi Lyu, Jiahao Shi, Qi Liu, Mingjun Jiang, Xilian Liu, Yulan Li, Shuqin Ding, Xianpeng Dai

“…The study provides, for the first time, the transcriptomic characteristics and immunological of the spleens of EPO treated mice, providing a new perspective for the study of the effects of EPO on mice.…”
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From spots to cells: Cell segmentation in spatial transcriptomics with BOMS. by Ocima Kamboj, Jeongbin Park, Oliver Stegle, Fred A Hamprecht

“…Imaging-based Spatial Transcriptomics methods enable the study of gene expression and regulation in complex tissues at subcellular resolution. …”
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TraV: a genome context sensitive transcriptome browser. by Sascha Dietrich, Sandra Wiegand, Heiko Liesegang

“…Next-generation sequencing (NGS) technologies like Illumina and ABI Solid enable the investigation of transcriptional activities of genomes. While read mapping tools have been continually improved to enable the processing of the increasing number of reads generated by NGS technologies, analysis and visualization tools are struggling with the amount of data they are presented with. …”
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Transcriptomic responses of sponge holobionts to in situ, seasonal anoxia and hypoxia by Strehlow, Brian W., Schuster, Astrid, Francis, Warren R., Eckford-Soper, Lisa, Kraft, Beate, McAllen, Rob, Nielsen, Ronni, Mandrup, Susanne, Canfield, Donald E.

“…Thaumarchaeota symbionts also upregulated stress response genes in hypoxia, while maintaining expression of oxygen-dependent metabolic pathways under hypoxia and anoxia. …”
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A spatial transcriptomic atlas of the host response to oropharyngeal candidiasis by Sunna Nabeela, Hayden McSwiggin, Rubens Daniel Miserani Magalhaes, Eliciane Cevolani Mattos, Mohammad Mannan, John T. Dillon, Ashley Barbarino, Eman G. Youssef, Shakti Singh, Wei Yan, Ashraf S. Ibrahim, Heather R. Conti, Priya Uppuluri

“…Our study used spatial transcriptomics, a cutting-edge technology that preserves tissue architecture while mapping immune interactions at high resolution. …”
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SpaNorm: spatially-aware normalization for spatial transcriptomics data by Agus Salim, Dharmesh D. Bhuva, Carissa Chen, Chin Wee Tan, Pengyi Yang, Melissa J. Davis, Jean Y. H. Yang

“…Abstract Normalization of spatial transcriptomics data is challenging due to spatial association between region-specific library size and biology. …”
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Practical steps to develop a transcriptomic test for blood doping by Sutehall Shaun, Malinsky Fernanda, Voss Sven, Chester Neil, Xu Xiao, Pitsiladis Yannis

“…., the athlete biological passport). While this has played a significant role in the protection of clean sport, improvements are needed. …”
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Mapping Human Uterine Disorders Through Single-Cell Transcriptomics by Sandra Boldu-Fernández, Carolina Lliberos, Carlos Simon, Aymara Mas

“…Single-cell RNA sequencing and spatial transcriptomics have mapped endometrial and myometrial cellular landscapes, which helped to identify critical cell types, signaling pathways, and phase-specific dynamics. …”
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Joint cell segmentation and cell type annotation for spatial transcriptomics by Russell Littman, Zachary Hemminger, Robert Foreman, Douglas Arneson, Guanglin Zhang, Fernando Gómez‐Pinilla, Xia Yang, Roy Wollman

“…Overall, our work demonstrates that known cell type expression patterns can be leveraged to improve the accuracy of RNA hybridization‐based spatial transcriptomics while providing highly granular cell (sub)type information. …”
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Reidentification of hybridization events with transcriptomic data and phylogenomic study in Seabuckthorn by Hui Zhang, Zhiqi Wang, Xue Su, Dong Han, Lujie Yang, Ying Zhang, Jing Fang, Jingyuan Wang, Kun Sun

“…Abstract Natural hybridization in sea buckthorn (Hippophae spp.) is well documented. While the parental species involved in these events have been identified, distinctions between F1 hybrids and later-generation (Fn) hybrids remain insufficiently explored, and their genetic compositions are not yet fully understood. …”
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Heterogeneity and longitudinal transcriptomic characteristics of Tregs in COVID-19 patients by Yanling Wen, Juanjuan Zhao, Zheng Zhang

“…Using transcriptomic analysis, we evaluated the proportion and functionality of different Treg subsets, specifically HLA_DR+ Tregs, across different stages of COVID-19 patients.ResultsOur analysis revealed that the proportion of CCR7+ Tregs decreased as the disease advanced, while the cell proportion of HLA_DR+ regs escalated with the severity of the disease. …”
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Furanocoumarins in two European species of Heracleum: transcriptomic and metabolomic study by Victoria Yu. Shtratnikova, Viktor P. Bogdanov, Mikhail I. Schelkunov, Anna V. Klepikova, Mariya A. Kulbachnaya, Ekaterina N. Obukhova, Elena V. Ptitsyna, Margarita A. Ezhova, Aleksey A. Penin, Maria D. Logacheva

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Hormonal and transcriptomic regulation of drought adaptation in barley roots and leaves by Anna Collin, Magdalena Pacwa-Plociniczak, Tomasz Plociniczak, Ôndrej Novak, Marek Marzec, Wenbin Guo, Craig G. Simpson, Agata Daszkowska-Golec

“…In leaves, drought primarily downregulated photosynthesis-related genes while upregulating pathways involved in water stress and abscisic acid (ABA) signaling. …”
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Meta-Transcriptomic Response to Copper Corrosion in Drinking Water Biofilms by Jingrang Lu, Ian Struewing, Nicholas J. Ashbolt

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Transcriptome analysis reveals regulatory mechanism of postharvest softening in kiwiberry by Zhao Liu, Yang Sun, Zhenpan Liu, Jianyu Song, Weicong Yang, Zhannan Wang, Taiming Liang, Dejun Liang

“…Results Morphological observations and analysis of physical parameters showed that the skin of kiwiberry did not change markedly from the 1st to the 7th day after harvest, while the colour of the inner pericarp gradually turned yellow. …”
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Oncogene-Induced Senescence Transcriptomes Signify Premalignant Colorectal Adenomas by Sofian Al Shboul, Heyam Awad, Anas Abu-Humaidan, Nidaa A. Ababneh, Ashraf I. Khasawneh, Tareq Saleh

“…Pairwise comparisons confirmed that 65% of patients exhibited higher OIS scores in adenomas, while SASP enrichment declined in 59–61% of cases. …”
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Transcriptomic Profiling of Hypoxia-Adaptive Responses in Tibetan Goat Fibroblasts by Lin Tang, Li Zhu, Zhuzha Basang, Yunong Zhao, Shanshan Li, Xiaoyan Kong, Xiao Gou

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The transcriptomic fingerprint of cancer response to Tumor Treating Fields (TTFields) by Kerem Wainer-Katsir, Adi Haber, Hila Fishman, Lianghao Ding, Michael D. Story, Renfei Du, Ulf D. Kahlert, Laura Mannarino, Federica Mirimao, Monica Lupi, Maurizio D’Incalci, Gitit Lavy-Shahaf, Hila Ene, Roni Frechtel-Gerzi, Zeina Drawshy, Antonia Martinez-Conde, Eyal Dor-On, Yaara Porat, Moshe Giladi, Uri Weinberg, Yoram Palti

“…In the current research we performed whole transcriptome analysis across tumor types to identify pan-cancer responses to TTFields. …”
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