Comprehensive physiological, transcriptomic, and metabolomic analyses revealed the regulation mechanism of evergreen and cold resistance of Pinus koraiensis needles by Yan Li, Xin Li, Dan Peng, Jiaxin Luo, Shuai Zhu, Haibo Du, Xiaoning Li, Jiafeng Zhang, Jun Meng, Xiaona Pei, Xiyang Zhao

“…The differential expression of transcription factor genes, including bHLH, MYB-related, AP2/ERF, C3H, and NAC, provides insights into the needles’ seasonal adaptations. …”
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Identification of key LncRNAs and mRNAs in fat deposition of Saba pigs based on comparative analysis of transcriptomics by Xinxing Dong, Xinpeng Li, Xiaoyi Wang, Qiang Chen, Mingli Li, Dawei Yan, Guoxiang Lan, Shaoxing Lu

“…In summary, this study provides a theoretical foundation and valuable insights into the molecular mechanisms underlying LncRNA-mediated regulation of fat deposition in pigs. …”
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Transcriptome and metabolome analyses reveal that GA3ox regulates the dwarf trait in mango (Mangifera indica L.) by Yu Zhang, Xinhua Pang, Mu Li, Ji Zhang, Ying Zhao, Yujuan Tang, Guodi Huang, Shaolong Wei

“…Results In this study, we compared the transcriptomes and metabolomes of mango varieties Guiqi (a dwarfed variety) and Jinhuang (an arborized variety). …”
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Comparative transcriptome analysis revealed the influence of sucrose on flavor and taste quality of Coffea arabica and C. canephora varieties by Lifang Huang, Lisong Hu, Yu Fan, Xiaoyang Wang, Yunping Dong, Fupeng Li, Yuzhou Long, Lin Yan, Jie Meng

“…The content of sucrose and its influence on the downstream secondary metabolism probably play important roles in the FT quality of coffee beans. Our results provide efficient targets for investigation regarding the influence of sucrose on FT quality of coffee beans.…”
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Metabolome and transcriptome reveal dynamic patterns of floral scent release and gene expression during flower development in carnation by Luhong Leng, Rui Huang, Zhiqiang Wu, Xiaoni Zhang

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A New Tool to Decrease Interobserver Variability in Biomarker Annotation in Solid Tumor Tissue for Spatial Transcriptomic Analysis by Sravya Palavalasa, Emily Baker, Jack Freeman, Aditri Gokul, Weihua Zhou, Dafydd Thomas, Wajd N. Al-Holou, Meredith A. Morgan, Theodore S. Lawrence, Daniel R. Wahl

“…Immunofluorescence provides information about protein expression at the cellular or subcellular level, whereas spatial transcriptomic platforms typically rely on multicellular “spots” for RNA profiling. …”
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Spatial transcriptomic analysis of 4NQO-induced tongue cancer revealed cellular lineage diversity and evolutionary trajectory by Feng Liu, Feng Liu, Xiaojun Wu, Shaoqing Yu, Deqiang Cheng, Jun Pan, Xiaodong Wang, Guanzhen Yu, Guanzhen Yu, Chaofu Li

“…Key findings include the identification of specific switch genes associated with tumor invasion and the revelation of significant intratumor heterogeneity.DiscussionThis spatial transcriptomic analysis of 4NQO-induced tongue cancer provides a detailed characterization of tumor evolution and heterogeneity. …”
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Transcriptomic Analysis of Venom Secretion in <i>Achelura yunnanensis</i>: Lipid Metabolism, Redox Reactions, and Structural Adaptations by Ping Liu, Hui-Qin Zhu, Si-Ming Wang, Yu-Qian Wang, Zhen-Yuan Ruan, Lu Qiao, Xing-Xing Wu, Qing-Hua Yan, Ya-Ping Lu, Bing Bai, Wei-Feng Ding

“…This study aimed to uncover the molecular mechanisms of venom secretion by comparing the dorsal epidermis tissue (LDET) with the larval proleg tissue (LP). We performed transcriptomic analysis using RNA sequencing to identify differentially expressed genes between LDET and LP (10 biological replicates per tissue type), followed by functional enrichment and gene expression correlation analyses to explore tissue-specific characteristics. …”
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De novo assembly of a transcriptome for Calanus finmarchicus (Crustacea, Copepoda)--the dominant zooplankter of the North Atlantic Ocean. by Petra H Lenz, Vittoria Roncalli, R Patrick Hassett, Le-Shin Wu, Matthew C Cieslak, Daniel K Hartline, Andrew E Christie

“…This is the first report of multiple NaV1 genes in a protostome. These data provide new insights into the transcriptome and physiology of this environmentally important zooplankter.…”
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Integration of GWAS and transcriptome analysis to identify temperature-dependent genes involved in germination of rapeseed (Brassica napus L.) by Ruisen Wang, Guangyu Wu, Jingyi Zhang, Weizhen Hu, Xiangtan Yao, Lixi Jiang, Yang Zhu

“…Through integrated analysis of transcriptome sequencing and GWAS, we identified a series of candidate genes involved in temperature-dependent germination. …”
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De Novo assembly of the Japanese flounder (Paralichthys olivaceus) spleen transcriptome to identify putative genes involved in immunity. by Lin Huang, Guiyang Li, Zhaolan Mo, Peng Xiao, Jie Li, Jie Huang

“…However, genomic and transcriptomic data for Japanese flounder remain scarce, which limits studies on the immune system of this species. …”
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Single-cell transcriptomics analysis reveals a disrupted NK-T cell interaction network in liver metastatic cancer by Xiaoshuang Wang, Zhongen Wu, Yan Zhou, Dehua Yang, Qingtong Zhou, Di Zhu, Ming-Wei Wang, Lu Wang

“…In this study, we analyzed single-cell transcriptomics of liver metastases and adjacent tissues from nasopharyngeal carcinoma (NPC), thyroid carcinoma (THCA), breast cancer (BC), colorectal cancer (CRC) and cervical cancer (CESC) to uncover the NK-T cell interaction network and its functional implications. …”
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Identification of lactylation-associated immune and metabolic regulators in bladder cancer via integrated bulk and single-cell transcriptomics by Yanjun Chen, Yu Sun, Xiaoyan Liu, Xiaoyan Liu

“…BackgroundLactate-driven metabolic reprogramming and histone lactylation play pivotal roles in bladder cancer (BLCA) progression, yet their underlying mechanisms and regulatory genes remain poorly understood.MethodsUsing transcriptomic data from The Cancer Genome Atlas (TCGA), we identified lactylation-associated genes and constructed a prognostic signature. …”
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Integrated transcriptome and metabolome analyses unraveled critical roles of small intestine during the weaning period of Vespertilio sinensis by Zixuan Li, Wei Guo, Yujia Chu, Xiao Tan, Hui Wang, Jiang Feng, Tong Liu

“…Conclusions This is the first study to investigate transcriptomic and metabolomic changes in the small intestine of insectivorous bats during weaning. …”
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Distinct expression of select and transcriptome-wide isolated 3'UTRs suggests critical roles in development and transition states. by Shaoyi Ji, Ze Yang, Leonardi Gozali, Thomas Kenney, Arif Kocabas, Carolyn Jinsook Park, Mary Hynes

“…Unbiased transcriptome analysis across multiple gene sets shows that regardless of tissue, genes with high 3'UTR to CDS ratios belong predominantly to gene ontology categories related to cell-type specific functions. …”
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Cross-Kingdom Pathogenesis of <i>Pantoea alfalfae</i> CQ10: Insights from Transcriptome and Proteome Analyses by Jing Su, Bo Yao, Rong Huang, Xiaoni Liu, Zhenfen Zhang, Yong Zhang

“…Thus, CQ10 is a plant and animal cross-kingdom pathogenic bacterium. Transcriptome and proteome analyses showed that biofilm and iron uptake are important virulence factors of the pathogen CQ10, among which <i>Bap</i> and <i>Lpp</i> regulating biofilm are the key cross-kingdom virulence genes of CQ10. …”
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Transcriptome immune-regulatory differences between leprosy patients and type 1 reaction patients, before onset of symptoms. by Wilian Correa-Macedo, Monica Dallmann-Sauer, Marianna Orlova, Jeremy Manry, Vinicius M Fava, Nguyen Thu Huong, Nguyen Ngoc Ba, Nguyen Van Thuc, Vu Hong Thai, Erwin Schurr

“…Combined, these results provided detailed insight into the pathogenesis of T1R.…”
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Molecular insights into region-specific sexual dichromatism: Comparative transcriptome analysis of red cheek pigmentation in zebra finches. by Gee-Way Lin, Chih-Kuan Chen, Ting-Xin Jiang, Ya-Chen Liang, Pin-Chi Tang, Ping Wu, Randall B Widelitz, Chih-Feng Chen, Cheng-Ming Chuong

“…We focus on sexual dichromatism of craniofacial plumage and use the male cheek domain of the zebra finch (Taeniopygia guttata) as the major model. The transcriptome of the cheek and scalp (crown) domains in males and females of wild-type and genetic color variants were compared. …”
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Differential photosynthetic responses to drought stress in peanut varieties: insights from transcriptome profiling and JIP-Test analysis by Jingyao Ren, Pei Guo, Xinhua Zhao, Xinlei Ma, Xin Ai, Jing Wang, Hongtao Zou, Haiqiu Yu

“…Conclusion These findings provide mechanistic insights into cultivar-dependent photosynthetic responses to drought stress, offering potential biomarkers for breeding drought-resilient peanut varieties.…”
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A rare IDH-Mutant glioma case: insights from single-cell transcriptomic analysis of tumor recurrences by Wen Li, Yuanshuai Zhou, Shaheryar Shafi, Jun Dong, Minxuan Sun

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