Epigenomic analysis identifies DTP subpopulation using HOPX to develop targeted therapy resistance in lung adenocarcinoma by Yang Tian, Reshmee Bhattacharya, Seungyeul Yoo, Feng Jiang, Eric Park, Genesis Lara Granados, Yudao Shen, Kwang-Su Park, Husnu Umit Kaniskan, Jian Jin, Benjamin D. Hopkins, Jun Zhu, Hideo Watanabe

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Epizootic shell disease induces systemic transcriptomic shifts in Homarus americanus, characterized by increased shell degradation and impaired energy metabolism across tissues by Minseo Kim, Dianjun Cao, Vincent Cavaleri, Kyudong Han, Kyudong Han, Kyudong Han, Seyoung Mun, Seyoung Mun, Seyoung Mun, Soo Jin Jeon

“…In this study, we investigated the effects of ESD on four major tissues of the lobster (testis, intestine, hepatopancreas, and green gland) using transcriptomic analysis. A total of 564 genes were differentially expressed in the testis, 105 in the intestine, 333 in the hepatopancreas, and 112 in the green gland. …”
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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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TraV: a genome context sensitive transcriptome browser. by Sascha Dietrich, Sandra Wiegand, Heiko Liesegang

“…In order to process fifteen transcriptome sequencing experiments of Bacillus licheniformis DSM13 obtained in a previous study, we developed TraV, a RNA-Seq analysis and visualization tool. …”
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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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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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Transcriptomic and metabolic changes during tassel branching development in maize by Yuxin Tai, Xiangling Lyu, Feng Pan, Lingzhi Meng, Zixiang Cheng, Zhennan Xu, Mingshun Li, Zhuanfang Hao, Degui Zhang, Hongjun Yong, Zhiqiang Zhou, Jienan Han, Xinhai Li, Jianfeng Weng

“…Integrated transcriptomic and metabolomic analysis revealed enrichment of the tryptophan metabolism, a crucial auxin biosynthetic pathway, suggesting its potential involvement in tassel branching development. …”
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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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Practical steps to develop a transcriptomic test for blood doping by Sutehall Shaun, Malinsky Fernanda, Voss Sven, Chester Neil, Xu Xiao, Pitsiladis Yannis

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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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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

“…Finally, we constructed the first phylogenomic tree of the Hippophae genus using transcriptomic data and performed a comparative analysis of interspecific relationships based on SNP and indel markers derived from the same dataset.…”
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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.

“…Nevertheless, both anoxia and hypoxia caused upregulation of heat shock proteins (HSPs), indicating cellular level adaptations to deoxygenation stress. A meta-analysis demonstrated that sponge transcriptional responses to anoxia were distinct from those displayed by other invertebrates while dormant, and the hypothesis of sponge dormancy under anoxia was not supported. …”
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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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Recent allopolyploidization and transcriptomic asymmetry in the mangrove shrub Acanthus tetraploideus by Wuxia Guo, Achyut Kumar Banerjee, Hui Feng, Wei Lun Ng, Haidan Wu, Weixi Li, Yang Yuan, Yelin Huang

“…While no strong evidence directly links transcriptomic changes to specific adaptive traits, the patterns in unbiased and novelly biased genes in A. tetraploideus suggest adaptations to stable polyploidy. …”
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Metabolic Plasticity and Transcriptomic Reprogramming Orchestrate Hypoxia Adaptation in Yak by Ci Huang, Yilie Liao, Wei Peng, Hai Xiang, Hui Wang, Jieqiong Ma, Zhixin Chai, Zhijuan Wu, Binglin Yue, Xin Cai, Jincheng Zhong, Jikun Wang

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A Transcriptomic Study on the Toxic Effects of Iodide (I⁻) Wet Deposition on Pepper (<i>Capsicum annuum</i>) Leaves by Rui Yu, Zhu-Ling Ma, Min Wang, Jie Jin

“…Using sodium iodide (NaI) as the exposure agent, transcriptomic analysis was conducted to evaluate the molecular responses of chili pepper leaves to iodine at concentrations of 2, 4, and 8 ppm. …”
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Multi-omics analysis of Iris sanguinea with distinctive flower colors provides insights into petal coloration by Guiling Liu, Huijun Liu, Gongfa Shi, Nuo Xu, Zhaoqian Niu, Lei Wang, Ruiyang Zhao, Ling Wang, Lijuan Fan

“…Integrated metabolomics and transcriptomics analysis further led to the discovery of molecular modules controlling petal pigmentation, in which an R2R3 MYB transcription factor IsMYBL1 was found to be associated with the accumulation of key anthocyanin derivatives, it localized to the nucleus. …”
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Therapeutic effects and mechanism analysis of Paeonia lactiflora extract (PLE) in menopausal rats with hot flashes by Weilin Cui, Tingting Song, Dongmei Gao, Xiaoyu Wang, Ya Sun, Liyu Fu, Yichao Han, Jieqiong Wang

“…The changes in facial and tail temperature of rats in each group were observed; the behavioral characteristics of rats in each group were followed by an open field test, elevated plus maze and aggressive behavior test; the contents of estradiol, luteinizing hormone, follicle stimulating hormone, 5-hydroxytryptamine, cyclic guanosine monophosphate and cyclic adenosine monophosphate were detected by ELISA; the pathological changes of the uterus were detected by HE staining method. Combined with transcriptomics technology, high-throughput transcriptome sequencing was performed on the hypothalamus of control, model and PLE (160 mg/kg) group, and differential gene analysis between control and model groups, and PLE (160 mg/kg) group and model group was performed using DESeq2. qRT-PCR and Western blot were used to further validate the candidate core genes.ResultsPLE improved the mental status of model rats and reduced the abnormal tail temperature elevation in model rats. …”
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Genetic Analyses, BSA-Seq, and Transcriptome Analyses Reveal Candidate Genes Controlling Leaf Plastochron in Rapeseed (<i>Brassica napus</i> L.) by Mengfan Qin, Xiang Liu, Jia Song, Feixue Zhao, Yiji Shi, Yu Xu, Zhiting Guo, Tianye Zhang, Jiapeng Wu, Jinxiong Wang, Wu Li, Keqi Li, Shimeng Li, Zhen Huang, Aixia Xu

“…The leaf plastochron serves as an indicator of the rate of leaf appearance, biomass accumulation, and branch number, while also impacting plant architecture and seed yield. …”
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