Transcriptomic Profiling Reveals Altered Expression of Genes Involved in Metabolic and Immune Processes in NDV-Infected Chicken Embryos by Malarmathi Muthusamy, Kannaki T. Ramasamy, Sunday Olusola Peters, Srinivasan Palani, Vasudevan Gowthaman, Murali Nagarajan, Sivakumar Karuppusamy, Vasanthakumar Thangavelu, Thiruvenkadan Aranganoor Kannan

“…It is essential to comprehend how the sequence of development affects biological pathways and how early exposure to infections might affect immune responses. Methods: This study employed transcriptome analysis to investigate host–pathogen interactions by analyzing gene expression changes in NDV-infected chicken embryos’ lungs. …”
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Root Transcriptome Analysis Identifies Salt-Tolerance Genes in Sweet Corn Chromosome Segment Substitution Lines (CSSLs) by Zili Zhang, Xuxuan Duan, Pengfei Liu, Qingchun Chen, Wei Sun, Xiaorong Wan, Yixiong Zheng, Jianting Lin, Feng Jiang, Faqiang Feng

“…Salt stress severely constrains global crop productivity. However, most sweet corn cultivars exhibit weak tolerance to salt stress. …”
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Effects of chlorogenic acid on growth performance, immunity, antioxidant capacity, intestinal microbiota, and liver transcriptome in Mauremys mutica by Hongyao Zhang, Jingu Shi, Zike Yan, Mingzuo Gao, Kaijie Lin, Yutian Zhan, Yuhan Li, Jingzhen Liang, Shuyu Han

“…Notably, the 200 mg/kg CGA treatment exhibited the most significant improvements in growth performance, digestive enzyme activity, intestinal morphology, villus length, immunity, and antioxidant capacity. …”
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Single-cell transcriptome analysis revealed a suppressive tumor immune microenvironment in EGFR mutant lung adenocarcinoma by Lei Yang, Qing Zhou, Bo Zhang, Yi-Long Wu, Zhi-Hong Chen, Wen-zhao Zhong, Fen Wang, Yun-Ting He, Song Dong, Xue-Wu Wei, Wei-Dong Chen, Xiao-Rong Yang, Xue-Meng Shang

“…Hence, we initiated this study to describe the specific TME of EGFR-mutant lung adenocarcinoma (LUAD) from cellular compositional and functional perspectives to better understand the immune landscape of this most common subtype of NSCLC.Methods We used single-cell transcriptome sequencing and multiplex immunohistochemistry to investigate the immune microenvironment of EGFR-mutant and EGFR wild-type LUADs and determined the efficacy of immunotherapy. …”
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Transcriptome Profiling Reveals the Effects of Rootstocks on Scion Architecture in <i>Malus domestica</i> Borkh Var. ‘Harlikar’ by Bin Xie, Junhao Li, Jiangtao Zhou, Guodong Kang, Zhongwen Tang, Xiaojian Ma, Xin Li, Jing Wang, Yanzhen Zhang, Yanhui Chen, Sumiao Yang, Cungang Cheng

“…The lowest plant height was observed in ‘Harlikar’/‘71-3-150’, only 50.47% of ‘Harlikar’/‘Qingzhen 2’ and 56.51% of ‘Harlikar’/‘<i>M. baccata</i>’, and the lowest internode length was observed in ‘Harlikar’/‘M9-Nic29’, only 60.76% of ‘Harlikar’/‘Qingzhen 2’ and 79.11% of ‘Harlikar’/‘<i>M. baccata</i>’. The transcriptome, weighted gene co-expression network and KEGG enrichment analyses revealed that, compared to ‘Harlikar’/‘<i>M. baccata</i>’, most differentially expressed genes screened from ‘Harlikar’/‘Qingzhen 2’, ‘Harlikar’/‘71-3-150’, and ‘Harlikar’/‘M9-Nic29’ were enriched in hormone signal transduction pathways. …”
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Transcriptional Dynamics Underlying Somatic Embryogenesis in <i>Coffea canephora</i> by Marcos-David Couoh-Cauich, Hugo A. Méndez-Hernández, Rosa M. Galaz-Ávalos, Ana Odetth Quintana-Escobar, Enrique Ibarra-Laclette, Víctor M. Loyola-Vargas

“…During the first few hours, the early response to induction occurs, characterized by the highest number of differentially expressed genes, most related to the response to multiple stimuli. …”
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Identification of Gene Pathways Involved in Tolerance to End-of-Season Drought Stress in the Dayton/Ranney Barley Genotype using Transcriptomics by Saeedeh Alidoust, Sara Dezhsetan, Mahdi Behnamian

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Correlates of clinical benefit from immunotherapy and targeted therapy in metastatic renal cell carcinoma: comprehensive genomic and transcriptomic analysis by Sumanta Pal, Paulo Gustavo Bergerot, Nazli Dizman, JoAnn Hsu, Yung Lyou, Nicholas Salgia, Daniel Enriquez, Tyler Izatt, Jeffrey M Trent, Sara Byron

“…The most commonly used IO and VEGF-TKIs were nivolumab (66%) and sunitinib (40%). …”
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Sequential transcriptome profiling: comparative analysis of normal and canine lymphoma preceding detailed T-cell and B-cell subtype comparison by Yeji Kim, Yeji Kim, Jihyun Kim, Jihyun Kim, Yunji Song, Yunji Song, Keunhwan Jang, Se Eun Kim, Se Eun Kim, Se Eun Kim, Ha-Jung Kim, Ha-Jung Kim

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Polyploidization-driven transcriptomic dynamics in Medicago sativa neotetraploids: mRNA, smRNA and allele-specific gene expression by D. F. Santoro, G. Marconi, S. Capomaccio, M. Bocchini, A. W. Anderson, A. Finotti, M. Confalonieri, E. Albertini, D. Rosellini

“…Several of these belong to classes involved in stress response. Small RNA-seq revealed that very few miRNAs were significantly associated with WGD, but they target several hundred genes, and their role in the WGD response may be relevant. …”
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Transcriptomic Profiling Reveals Differences in Slow‐Twitch and Fast‐Twitch Muscles of a Cigarette Smoke‐Exposed Rat Model by Timothy K. H. Fung, Kwok Kuen Cheung, Xia Wang, Benson W. M. Lau, Shirley P. C. Ngai

“…ABSTRACT Background Cigarette smoking is known to affect muscle function and exercise capacity, including muscle fatigue resistance. Most studies showed diminished cross‐sectional area and fibre type shifting in slow‐twitch muscles such as the soleus, while effects on fast‐twitch muscles were seldom reported and the differential responses between muscle types in response to exposure to cigarette smoke (CS) were largely unknown. …”
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A systematic review on the trend of transcriptomic study in livestock: An effort to unwind the complexity of adaptation in a climate change environment by Putri Kusuma Astuti, Péter Sárkány, George Wanjala, Zoltán Bagi, Szilvia Kusza

“…Our analysis demonstrates the growing popularity and application of transcriptome approaches in the investigation of the response of ruminants, pigs, and poultry livestock to heat stress. …”
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A Strain Capable of Reducing Aflatoxin B1: Identification, Optimization of Removal Conditions and Transcriptomic Analysis of Degradation Pathways by WANG Lihui, PEI Yangyang, CHEN Xiaoru, ZHAO Huan, LIU Shuliang, HU Kaidi, ZHAO Ning, LI Qin, LI Jianlong

“…The removal conditions of AFB1 by this strain were optimized and important physiological and metabolic processes were elucidated using transcriptomics. The results single factor experiments indicated that pH, temperature, and inoculum size had the most significant influence on the degradation rate of AFB1. …”
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Comparative single‐cell transcriptomic profiling of patient‐derived renal carcinoma cells in cellular and animal models of kidney cancer by Richard Huang, Lynn Kee, Alexander Gont, Jalna Meens, Fraser G. Ferens, Meredith S. Irwin, Laurie Ailles, Scott A. Yuzwa, Claire M. Robinson, Michael Ohh

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Temporal transcriptomic changes in the THY-Tau22 mouse model of tauopathy display cell type- and sex-specific differences by Muhammad Ali, Pierre Garcia, Laetitia P. Lunkes, Alessia Sciortino, Melanie H. Thomas, Tony Heurtaux, Kamil Grzyb, Rashi Halder, Alexander Skupin, Luc Buée, David Blum, Manuel Buttini, Enrico Glaab

“…Objective To understand sex-specific and sex-dimorphic transcriptomic changes in different cell types and their age-dependence in the THY-Tau22 mouse model of AD-linked tauopathy. …”
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Effects of defined voluntary running distances coupled with high‐fat diet consumption on the skeletal muscle transcriptome of male mice by Afrina Brishti, Sarah J. Johnson, Daniel G. Palmer, Md Obayed Raihan, Lin Yan, Shanon L. Casperson

“…However, complex molecular changes that occur in skeletal muscle in response to exercising while consuming a HFD are not yet known. …”
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Patient-centered brain transcriptomic and multimodal imaging determinants of clinical progression, physical activity, and treatment needs in Parkinson’s disease by Quadri Adewale, Ahmed Faraz Khan, Sue-Jin Lin, Tobias R. Baumeister, Yashar Zeighami, Felix Carbonell, Daniel Ferreira, Yasser Iturria-Medina

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Time-coexpress: temporal trajectory modeling of dynamic gene co-expression patterns using single-cell transcriptomics data by Shuyi Yang, Anderson Bussing, Giampiero Marra, Michelle L. Brinkmeier, Sally A. Camper, Shannon W. Davis, Yen-Yi Ho

“…Abstract Background The rapid advancement of single-cell RNA sequencing (scRNAseq) technology provides high-resolution views of transcriptomic activity within individual cells. Most routine analyses of scRNAseq data focus on individual genes; however, the one-gene-at-a-time analysis is likely to miss meaningful genetic interactions. …”
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The blood transcriptome of musk deer under heat stress condition reveals the regulatory mechanism of genes to maintain homeostasis metabolism by Xin Shi, Zhuo Cheng, Chengli Zheng, Kaiqing Wang, Jiandong Yang, Hang Jie, Yang Li, Ming Zhang

“…Among them, JAK1, AP3B1 and FKBP15 were the most significantly up-regulated immune-related genes in response to heat stress. …”
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Single-cell and bulk transcriptome sequencing identifies circadian rhythm disruption and cluster-specific clinical insights in colorectal tumorigenesis by Chen Liu, Jingyang Liu, Jing Shao, Xiaoman Zhao, Lin Xie, Mengyao Shang, Ying Li, Weiming Li

“…Abstract Background Colorectal cancer (CRC) is one of the most common malignant tumors in the digestive system worldwide, with its mortality ranking second among all cancers. …”
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