Inflammatory profiling and immune cell infiltration in dysthyroid optic neuropathy: insights from bulk RNA sequencing by Qintao Ma, Yuanping Hai, Yongbo Duan, Genfeng Yu, Cheng Song, ShengAi Huang, Anqi Huang, Yan Zhu, Yongzhi Shen, Zimeng Huang, Xiao Wang, Lan Liu, Thomas Efferth, Huiyu Guo, Yi Wang, Yi Wang, Jie Shen

“…WGCNA further identified key gene modules associated with inflammation and tissue remodeling in DON, and IRDCGs, such as CCL21, HP, and SLCO2A1, emerged as the most significant markers. Single-gene GSEA confirmed that these genes are involved in immune response, inflammation, and fibrosis-related processes. …”
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Biochemical and transcriptomic profiling analysis of drought tolerant related genes in ML 82-2 and ML 125-2 rice mutant lines by Jun Ying Low, Rhun Yian Koh, Sobri Hussein, Ahmad Faiz, Anna Pick Kiong Ling

“…The identified genes in both mutant lines are associated with drought resistance, with most sharing a similar genomic profile with MR220. …”
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Transcriptome and Coexpression Network Analyses Provide Insights into the Resistance of Chinese Cabbage During Different Stages of <i>Plasmodiophora brassicae</i> Infection by Huishan Liu, Lili Wang, Guozheng Wang, Haidong Wu, Xin Wang

“…These findings offer a valuable resource for further investigation of the immune response in the resistance of “JJ S5-1” to clubroot disease.…”
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Single-cell and spatial transcriptomic analyses revealing tumor microenvironment remodeling after neoadjuvant chemoimmunotherapy in non-small cell lung cancer by Xiaolu Cui, Siyuan Liu, He Song, Jingjing Xu, Yanbin Sun

“…Abstract Non-small cell lung cancer (NSCLC) represents the most common pathological type of lung cancer, and the combination of neoadjuvant immunotherapy with chemotherapy has emerged as the first-line treatment for NSCLC. …”
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Transcriptome-wide identification and analysis reveals m6A regulation of metabolic reprogramming in shrimp (Marsupenaeus japonicus) under virus infection by Xumei Sun, Yu-Lei Chen, Fan Xin, Siyuan Zhang

“…Abstract Background It has been reported that the most common post-transcriptional modification of eukaryotic RNA is N6-methyladenosine (m6A). …”
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Transcriptome Analysis Reveals the Molecular Mechanisms for Mycorrhiza-Enhanced Drought Tolerance in Maize by Regulating the Ca²⁺ Signaling Pathway by Qiaoming Zhang, Wenjing Yang, Miaomiao Wang, Junwei Chen, Zhaoran Zhang, Yanan Wei, Qingshan Chang, Minggui Gong

“…The annotation and enrichment of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) showed that most of the DEGs were significantly enriched in Ca²⁺ signaling pathway genes, related to signal transduction, cellular process, and defense response. …”
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A first de novo transcriptome assembly of feijoa (Acca sellowiana [Berg] Burret) reveals key genes involved in flavonoid biosynthesis by Hector Oberti, Juan Gutierrez‐Gonzalez, Clara Pritsch

“…They also play a crucial role in plant immune response. Despite their importance, the lack of research on A. sellowiana genomics and transcriptomics hinders a deeper understanding of the molecular mechanisms behind flavonoid biosynthesis and its regulation. …”
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RNA-Seq Analysis Uncovered Transcriptomic Changes in <i>Poncirus trifoliata</i> Roots Under Long-Term Soil Drought Conditions by Chuncao Song, Xingying Zeng, Lin Zheng, Qin Huang, Lingshan Zhong, Yong Zhou, Hengfu Yin, Yanjie Peng

“…These findings supplement the transcriptomic response of <i>P. trifoliata</i> root under long-term drought stress.…”
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Single-cell and bulk transcriptome analyses reveal elevated amino acid metabolism promoting tumor-directed immune evasion in colorectal cancer by Tianyue Sun, Yan Chen, Ying-Xuan Chen

“…IntroductionColorectal cancer (CRC), the third most common cancer worldwide, often shows limited responsiveness to immunotherapy due to its predominantly immune-excluded phenotype. …”
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Whole blood transcriptome changes following controlled human malaria infection in malaria pre-exposed volunteers correlate with parasite prepatent period. by Julian Rothen, Carl Murie, Jason Carnes, Atashi Anupama, Salim Abdulla, Mwajuma Chemba, Maxmillian Mpina, Marcel Tanner, B Kim Lee Sim, Stephen L Hoffman, Raphael Gottardo, Claudia Daubenberger, Ken Stuart

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Comparative transcriptome analysis of pectoralis major muscles affected by white striping, wooden breast and spaghetti meat in male and female broiler chickens by Marija Bošković Cabrol, Marianna Pauletto, Mery Giantin, Mauro Dacasto, Gerolamo Xiccato, Angela Trocino

“…Conclusions This study highlights marked sex-specific differences in molecular responses to WS, WB, and SM, with males exhibiting more pronounced transcriptomic alterations. …”
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Physio-biochemical and transcriptomics analyses reveal molecular mechanisms of enhanced UV-B stress tolerance in rice induced by titanium dioxide nanoparticles by Raheel Shahzad, Putri Widyanti Harlina, Shahid Ullah Khan, Muhammad Ihtisham, Aamir Hamid Khan, Fohad Mabood Husain, Agung Karuniawan

“…This study investigates the physiological and transcriptome responses in rice exposed to titanium dioxide nanoparticles (TiO2 NPs) under UV-B radiation. …”
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Transcriptomic Profiling Reveals Key Gene in <i>Trichoderma guizhouense</i> NJAU4742 Enhancing Tomato Tolerance Under Saline Conditions by Huiling Mei, Tuo Li, Haiyan Wu, Yanwei Xia, Qiwei Huang, Dongyang Liu, Qirong Shen

“…A forward mutant strain (designated M15) displaying near-complete loss of salt tolerance was successfully isolated. Comparative transcriptomic analysis between the wild type (wt) and M15 identified gene <i>Tgmfs</i>, a salt stress-responsive gene belonging to the major facilitator superfamily. …”
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Design and synthesis of 3,4-seco-lupane triterpene-tryptamine derivatives and revealing their anti-bladder cancer mechanisms by combining TCGA and transcriptomic approaches by Qinglong Chi, Hongbo Teng, Yaru Zhao, Xv Wang, Jiexin Zhang, Huiyue Shen, Xuan He, Yan Zhao, Chunxi Wang

“…Abstract Bladder cancer is the most common malignant tumor of the urinary tract. …”
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Time course transcriptomic profiling suggests Crp/Fnr transcriptional regulation of nosZ gene in a N2O-reducing thermophile by Jiro Tsuchiya, Sayaka Mino, Fuki Fujiwara, Nao Okuma, Yasunori Ichihashi, Robert M. Morris, Brook L. Nunn, Emma Timmins-Schiffman, Tomoo Sawabe

“…Here, we attempt to understand molecular responses of HRV44T to N2O. Time course transcriptome and proteomic mass spectrometry analyses under anaerobic conditions revealed that most of transcripts and peptides related to denitrification were constitutively detected, even in the absence of any nitrogen oxides as electron acceptors. …”
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TREM2 in MASH: integrating lipid metabolism and immune response by Shuyi Shi, Yangyang Zhou, Haiming Zhang, Junli Zhang

“…Metabolic dysfunction-Associated Steatohepatitis (MASH), a progressive liver disease characterized by disturbances of lipid metabolism and chronic inflammation response in liver has become the most prevalent chronic liver diseases worldwide. …”
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Integrative transcriptomic and proteomic analyses reveal that carbon metabolism and complement system of Madin Darby Bovine Kidney cells are affected by bovine coronavirus infectio... by Hui Zhang, Qisheng Yu, Rui Guo, Qing Zhu, Jin Yu, Zhaohui Zhang, Lan Lan, Cheng Tang, Changqing Yu, Bin Zhang

“…Following GO annotation and KEGG enrichment analysis, most DEGs and DEPs were significantly enriched in metabolic pathways, endocytosis, ribosome and protein processing in endoplasmic reticulum, apoptosis and immune response. …”
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Immunometabolic changes in macrophages in response to house dust mite extract by T. R. Yurakova, E. A. Gorshkova, M. A. Nosenko, E. O. Gubernatorova, M. S. Drutskaya

“…It was shown that the pathogenesis of allergic asthma in response to one of the most common allergens, house dust mite, is due to a metabolic TNF-mediated reprogramming of alveolar macrophages. …”
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Deciphering mitochondrial dysfunction in keratoconus: Insights into ACSL4 from machine learning-based bulk and single-cell transcriptome analyses and experimental validation by Yuchen Cai, Tianyi Zhou, Xueyao Cai, Wenjun Shi, Hao Sun, Yao Fu

“…Single cell sequencing data highlighted ACSL4 as the most promising biomarker, primarily expressed in corneal stromal cells (CSCs). …”
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A single-cell transcriptome analysis reveals astrocyte heterogeneity and identifies CHI3L1 as a diagnostic biomarker in Parkinson's disease by Zhongying Gong, Dan Guo, Yufeng Lin, Zhiwei Liu, Mengdi Lv, Xinxin Liu, Yang Yao, Sijia Wang, Yuan Wang, Zhiyun Wang

“…Background: Parkinson's disease (PD) is the second most common neurodegenerative disease, characterized by motor and non-motor symptoms. …”
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