Physiological response and transcriptomic analysis of red-fleshed apple seedlings to low temperature stress by LingYu Meng, Rui Zhang, YanPing Wei, Tingting Gu, Jiahao Zhao, Zijing Chen, Zongying Zhang, Nan Wang, Xuesen Chen, Wenjun Liu

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Spatial transcriptomic analysis of tumor microenvironment in esophageal squamous cell carcinoma with HIV infection by Yuanli Zuo, Yang Jin, Gang Li, Yue Ming, Ting Fan, Yitong Pan, Xiaojun Yao, Yong Peng

“…Methods We performed spatial transcriptome sequencing on HIV-ESCC samples to depict the microenvironment and employed cell communication analysis and multiplex immunofluorescence to investigate the molecular mechanism in HIV-ESCC. …”
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Transcriptome reveals the landscape of alveolar macrophages exposed to combined hypoxia with cigarette smoke extract by Qing Liu, Yushi Zhang, Ruirui Duan, Wanheng Li, Xuan Hou, Yiling Chen, Baicun Li, Ting Yang

“…Abstract Background Chronic obstructive pulmonary disease (COPD) is a complex and heterogeneous chronic inflammatory disease that is one of the leading causes of age-standardised deaths globally. While studies have investigated altitude's effects on COPD, none have explored alveolar macrophage homeostatic alterations during its pathogenesis at high altitudes. …”
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Transcriptome analysis of jejunal mucosal tissue in breeder hens exposed to acute heat stress by Yongcai Zhu, Satoshi Kubota, Phocharapon Pasri, Sitthipong Rakngam, Supattra Okrathok, Chayanan Pukkung, Shenglin Yang, Sutisa Khempaka

“…Transcriptome analysis revealed 138 genes with altered expression patterns under acute HS conditions. …”
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Global transcriptome modulation by xenobiotics: the role of alternative splicing in adaptive responses to chemical exposures by Andrew J. Annalora, Jacki L. Coburn, Antony Jozic, Patrick L. Iversen, Craig B. Marcus

“…Results Endpoint PCR revealed a Cyp2b2v to wild-type Cyp2b2 splicing ratio near 1:1 (100%) under most conditions, while RNA-seq showed a stable baseline closer to 40%. …”
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Analysis of Lipid Metabolism and Transcriptome Differences Before and After Wax Loading in Wax Gourd by Jinqiang YAN, Zhenqiang CAO, Jiesheng HONG, Piaoyun SUN, Wenrui LIU, Dasen XIE, Biao JIANG

“…Totally, 343 genes were found differentially expressed in the fruit peel of wax gourd inbred line 'P131' at 10 and 20 days after pollination, among which 120 were up-regulated while the other 223 were down-regulated based on transcriptome analysis, and CER1, TPS and other genes previously reported involved in wax formation were included. …”
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PM2.5 Induces Cell-Specific Transcriptomic Alterations in the Lungs of Juvenile Mice by Gui B, Li Y, Li K, Wang J, Fan W, Li L, Wu Q, Chen H

“…Among non-immune cells, ciliated cells activated interferon signaling, while adventitial fibroblasts showed increased ribosomal protein translation and calcium ion channel regulation. …”
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Exploring the Shared Genetic Characteristics of Peri-Implantitis and Osteoporosis: A Transcriptomic Analysis Perspective by Churen Zhang, Feixiang Wang, Jianguo Ke, Cuihong Lin, Xiaohua Zeng, Qiuyan Yang, Qiaoling Cai

“…Functional enrichment analysis revealed that intersected DEGs are involved in regulating oxidative stress, lipid metabolism, and osteoclast differentiation, while immune cell infiltration analyses highlighted correlations between gene expression and various immune cell types. …”
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Phenotypic differences and transcriptomic analysis of extreme plant heights in a hybrid population of Hedychium by Xuanguo LIANG, Fang WANG, Yunyi YU, Yanping FAN

“…Thirteen genes related to plant height regulation with significant differential expression were screened out based on transcriptome data. Among them, HcMYB136, HcNAC140, HcEXPA4, HcEXPB3, HcXTH28, HcXTH8, HcCYCB1-1 and HcCYCD3-2 were down-regulated in the three extremely dwarf plants, while HcMYB238, HcMYB254, HcNAC126, HcbZIP50 and HcCDC27B were up-regulated in the three extremely dwarf plants. …”
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Differential transcriptome study on the damage of testicular tissues caused by chronic infection of T. gondii in mice by Haoxin Li, Hao Yuan, Zi-Peng Yang, Yining Song, Jun-Jie Wang, Qingyuan Wen, Yu-Xiang Zheng, Xiu-Xiang Zhang, Miao Yu, Zi-Guo Yuan

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Transcriptome analysis reveals the mechanism of mixed oligosaccharides in the response of rice seedlings to abiotic stresses by Yanan Xu, Yanan Xu, Yigang Yang, Yeran Bai, Makoto Saito, Wei Han, Yuanpei Zhang, Guohua Lv, Jiqing Song, Wenbo Bai

“…Our findings demonstrated that KP-priming initiated a self-regulatory mechanism in plants, orchestrating a dual protective response that simultaneously mitigated oxidative damage while enhancing photosynthetic efficiency and stress resilience. …”
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Transcriptomic analysis of melatonin on the mechanism of embryonic gonadal development in female Jilin white geese by Jin Yu, Ichraf Mabrouk, Qiuyuan Liu, Yuxuan Zhou, Yupu Song, Jingyun Ma, Fengshuo Liu, Xiangman Hu, Zhiyi Yang, Yuxia Zeng, Jingtao Hu, Yongfeng Sun

“…The results showed that the in Ovo injection of melatonin increased the expression of FOXL2 in the gonads while decreasing the expression of CYP19A1. Transcriptome analyses revealed that a total of 1184 differentially expressed genes were screened in Jilin white goose embryonic gonads among the two comparison groups. …”
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Comprehensive Transcriptome Sequencing and Analysis of <i>Euspira gilva</i>: Insights into Aquaculture and Conservation by Zhixing Su, Jiayuan Xu, Xiaokang Lv, Xuefeng Song, Yanming Sui, Benjian Wang, Xiaoshan Wang, Bianbian Zhang, Baojun Tang, Liguo Yang

“…Predictive analysis of coding DNA sequences (CDS) resulted in 1340 BLAST comparisons, while ESTScan predicted 840. Further, 530 long non-coding RNAs (lncRNAs) were identified through the application of the CPC2, CNCI, Pfam, and PLEK algorithms. …”
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Increased reflux secondary bile acids are associated with changes to the microbiome and transcriptome in Barrett’s esophagus by Ceylan Tanes, Yun Li, Gary W. Falk, Gregory G. Ginsberg, Kenneth K. Wang, Prasad G. Iyer, Charles J. Lightdale, Armando Del Portillo, Stephen M. Lagana, Timothy C. Wang, Anil K. Rustgi, Michael Quante, Zhezhen Jin, Gary D. Wu, Elliot S. Friedman, Kyle Bittinger, Hongzhe Li, Julian A. Abrams

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Transcriptomic insights into early mechanisms underlying post-chikungunya chronic inflammatory joint disease by Mariana Severo Ramundo, Guilherme Cordenonsi da Fonseca, Felipe Ten-Caten, Alexandra L. Gerber, Ana Paula Guimarães, Erika Regina Manuli, Marina Farrel Côrtes, Geovana Maria Pereira, Otavio Brustolini, Milena Gomes Cabral, Carolina Dos Santos Lázari, Patrícia Brasil, Clarisse da Silveira Bressan, Helder I. Nakaya, Gláucia Paranhos-Baccalà, Ana Tereza R. Vasconcelos, Ester Cerdeira Sabino

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Establishment of somatic embryogenesis regeneration system and transcriptome analysis of early somatic embryogenesis in litchi by Yaqi Qin, Bo Zhang, Shiqian Wang, Wuyan Guo, Zhike Zhang, Yonghua Qin, Jietang Zhao, Guibing Hu

“…For somatic embryo (SE) induction, MS medium containing 0.5 g L−1 activated charcoal (AC) was the most effective, while the use of zeatin (ZT) and thidiazuron (TDZ) resulted in abnormal somatic embryos. …”
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Proinflammatory transcriptomic and kinomic alterations in astrocytes derived from patients with familial Alzheimer's disease by Benjamin Siciliano, Nicholas D. Henkel, William G. Ryan V, Ali Sajid Imami, John M. Vergis, Chongchong Xu, Taylen O. Arvay, Smita Sahay, Priyanka Pulvender, Abdul-rizaq Hamoud, Chadwick Hales, Robert E. McCullumsmith, Zhexing Wen

“…Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by profound neuronal and cognitive decline, with increasing evidence implicating astrocyte dysfunction in disease pathology. While traditional therapeutic approaches have primarily targeted neurons, the crucial role of astrocytes in metabolism, neurotransmission, amyloid-beta clearance, and neuroinflammation underscores their potential as therapeutic targets. …”
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Unravelling the transcriptomic landscape of primary lymphocytic scarring alopecias: systematic review and meta-analysis by Irene Rivera-Ruiz, Irene Rivera-Ruiz, Benjamin Ungar, Viviana Dávila-Flores, Jesús Gay-Mimbrera, Pedro J. Gómez-Arias, Pedro J. Gómez-Arias, Miguel Juan-Cencerrado, Miguel Juan-Cencerrado, Carmen Mochón-Jiménez, Carmen Mochón-Jiménez, Esmeralda Parra-Peralbo, Beatriz Isla-Tejera, Beatriz Isla-Tejera, Teresa López-Viñau López, Teresa López-Viñau López, Emma Guttman-Yassky, Juan Ruano, Juan Ruano

“…FFA and LPP showed strong immune activation, while CCCA exhibited lower inflammation but increased mitochondrial stress, lipid metabolism disruption, and fibroblast-associated remodeling. …”
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Genomic and Transcriptomic Profiles in Smokers and Never-Smokers Lung Squamous Cell Carcinoma Patients by Canale M, Virga A, Angeli D, Fonzi E, Gnetti L, Dubini A, Tedaldi G, Urbini M, Bocchialini G, Petracci E, Verlicchi A, Cravero P, Citarella F, Bennati C, Andrikou K, Delmonte A, Crinò L, Carbognani P, Ulivi P, Ampollini L

“…Enrichment analyses showed that cyclin-dependent protein Ser/Thr kinase activity and PI3K signaling pathways were affected in both groups, while cellular damage response was exclusively altered in never-smokers. …”
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Transcriptome analysis of Aedes aegypti midgut and salivary gland post-Zika virus infection by Chunling Zhu, Yuting Jiang, Qianghui Zhang, Jian Gao, Chaojie Li, Chunxiao Li, Yande Dong, Dan Xing, Hengduan Zhang, Teng Zhao, Xiaoxia Guo, Tongyan Zhao

“…Our findings demonstrate that Ae. aegypti exhibit distinct transcriptomic changes in response to ZIKV infection. …”
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