Dissecting tumor cell programs through group biology estimation in clinical single-cell transcriptomics by Shreya Johri, Kevin Bi, Breanna M. Titchen, Jingxin Fu, Jake Conway, Jett P. Crowdis, Natalie I. Vokes, Zenghua Fan, Lawrence Fong, Jihye Park, David Liu, Meng Xiao He, Eliezer M. Van Allen

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Wolbachia infections in Anopheles gambiae cells: transcriptomic characterization of a novel host-symbiont interaction. by Grant L Hughes, Xiaoxia Ren, Jose L Ramirez, Joyce M Sakamoto, Jason A Bailey, Anne E Jedlicka, Jason L Rasgon

“…Anopheles mosquitoes, which transmit human malaria parasites, have never been found to harbor Wolbachia in nature. While transient somatic infections can be established in Anopheles, no stable artificially-transinfected Anopheles line has been developed despite numerous attempts. …”
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Comparative transcriptome analysis of low- and high-latitude populations of Charybdis japonica under temperature stress by Shaolei Sun, Zhiqi He, Feijun Zhang, Zhiqiang Han

“…These results implied that the low-latitude population was more resilient to high-temperature stress, while the high-latitude population was more resilient to low-temperature stress. …”
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Integrative transcriptomic and metabolomic analysis explores the mechanisms by which ACT001 treats MAFLD in mice by Jing Liu, Yibing Zhou, Yinglun Li, Ze Chen, Xue Jiao, Jingqin Hu, Qian Wei, Yuqiang Mi, Ping Li

“…Histological analysis was performed, and liver enzyme and lipid levels were measured. Transcriptomic analysis was performed to identify differentially expressed genes, while metabolomic analysis was used to detect differential metabolites. …”
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Transcriptomic Responses to Rapid Cold Hardening in Tomato Leafminer Adults: Implications for Tomato Leafminer Management by Yan Zhao, Farman Ullah, Jiayi Shi, Yingjie Hu, Yuyang Jiang, Youming Hou

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Identifying KLF14 as a potential regulatory factor in liver regeneration trough transcriptomic and metabolomic by Chang Liu, Dalong Zhu, Junlong Xue, Alimu Tulahong, Tuerganaili Aji

“…Peripheral blood samples were collected from three patients undergoing PH and three patients undergoing ELRA at three time points: pre-operation, postoperative day 1, and postoperative day 5, as well as three healthy controls. Transcriptomic analysis was performed to identify differentially expressed genes (DEGs) using RNA sequencing, while metabolomic analysis was conducted using untargeted liquid chromatography-mass spectrometry (LC–MS). …”
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Combined transcriptomics and metabolomics to reveal the effects of copper exposure on the liver of rainbow trout(Oncorhynchus mykiss) by Junhao Lu, Jinqiang Quan, Jing Zhou, Zhe Liu, Jieping Ding, Tingting Shang, Guiyan Zhao, Lanlan Li, Yingcan Zhao, Xiangru Li, Jiajun Wu

“…We investigated the effects of Cu2+(75 μg/L, 150 μg/L, and 300 μg/L) on the rainbow trout liver. Combination of transcriptome and metabolome analyses, the regulatory mechanisms of the liver under Cu stress were elucidated. …”
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Identification and validation of differentially expressed genes in allergic asthma pathogenesis using whole-transcriptome sequencing by Fang Cui, Rui Liu, Li Wang, Jing He, Yanxia Xu

“…Inflammatory-related genes such as IL1B, CCL17, and MUC5AC were significantly upregulated in the patient group (p < 0.05), while regulatory immune factors such as FOXP3 and IFNG showed significantly higher expression in the control group (p < 0.05). …”
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Estimating the effect of tissue- and blood-derived cell reference matrices on deconvolving bulk transcriptomic datasets by Siqi Sun, Shweta Yadav, Mulini Pingili, Dan Chang, Jing Wang

“…Cell deconvolution is a widely used method to characterize the composition of the mixed cell population in bulk transcriptomic datasets. While tissue- and blood-derived cell reference matrices (CRMs) are commonly used, their impact on deconvolution accuracy has yet to be systematically evaluated. …”
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Transcriptome Profiling Revealed Light-Mediated Gene Expression Patterns of Plants in Forest Vertical Structures by Qiming Mei, Yi Zheng, Jiayi Feng, Zhengfeng Wang, Honglin Cao, Juyu Lian

“…Also, the expression of light-harvesting and photoprotection genes were generally up-regulated by intense light, while the expression of photoreceptor genes was up-regulated by shade. …”
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Transcriptome and Metabolome Analysis of Organic and Chemical Fertilizer Effects on Highland Barley Growth and Nutrient Utilization by Jiahui Yan, Hua Weng, Lu Hou, Qiang Yao, Tao He

“…The crop yields at harvest were not diminished in the combined fertilizer group compared to the OFR0 treatment group, while simultaneously achieving a 60% reduction in chemical fertilizer application. …”
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Metabolite and Transcriptomic Changes Reveal the Cold Stratification Process in <i>Sinopodophyllum hexandrum</i> Seeds by Rongchun Ning, Caixia Li, Tingting Fan, Tingting Ji, Wenhua Xu

“…Notably, cytokinins (CKs) and gibberellins (GAs) exhibited synergistic effects, while abscisic acid (ABA) displayed antagonistic effects. …”
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Molecular mechanisms after optic nerve injury: Neurorepair strategies from a transcriptomic perspective by Xiaxue Chen, Muyang Wei, Guangyu Li

“…This review focuses on optic nerve crush and glaucoma models, elucidating the mechanisms of optic nerve injury and neuron degeneration induced by glaucoma through single-cell transcriptomics, transcriptome analysis, and chip analysis. …”
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Dissecting pre- to post-implantation transition of DNA methylome-transcriptome dynamics in early mammalian development by Qingyuan Zhu, Ying Liu, Xin Hao, Shengyi Yan, Jitao Ge, Changqing Zheng, Xianwen Ren, Fan Zhou

“…The epigenome dynamics such as DNA methylome and transcriptome of embryos have been analyzed, while the coordination between these two molecular layers controlling lineage fate remained elusive. …”
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The rat mammary gland undergoes dynamic transcriptomic and lipidomic modifications from pre-puberty to adulthood by David Tovar-Parra, Alec McDermott, Melany N. Juarez, Jysiane Cardot, Mame Sokhna Sylla, Line Berthiaume, Géraldine Delbès, Martin Pelletier, Étienne Audet-Walsh, Isabelle Plante

“…Abstract Mammary gland development is a complex process involving dynamic interaction between the epithelial and stromal components at different critical stages, particularly around puberty. While epithelial tissue changes are well-documented, stromal mechanisms are less understood. …”
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Transcriptomic Deconvolution in Acute Myocardial Infarction: Exploring Diagnostic Potential and Validation Through Blood Counts by Murilo de Queiroz Ramos, José Victor Almeida Guimarães, Diego Moura Tanajura, Kiyoshi Ferreira Fukutani, Hanjia Gao

“…The keyword “myocardial infarction” was searched in the Gene Expression Omnibus database, and only transcriptomes from peripheral blood studies of patients with AMI within 12 h of symptom onset were included. …”
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Transcriptomic analysis reveals shared deregulated neutrophil responses in COVID-19 and idiopathic pulmonary fibrosis by Georgios Divolis, Evgenia Synolaki, Rodoula Tringidou, Argyrios Tzouvelekis, Dimitrios T. Boumpas, Panagiotis Skendros, Ioanna-Evdokia Galani

“…Additionally, pathways associated with autophagy and chromatin remodeling were upregulated, while translation-related processes were suppressed, indicating an increased predisposition for neutrophil extracellular trap (NET) release. …”
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Physiological, biochemical, and transcriptomic responses to waterlogging stress in Panicum bisulcatum, an emerging weed in rice fields by Jinqiu Sun, Xiaoyue Yu, Yongjie Yang, Hongxing Xu, Mengjie Liu, Zhongxian Lü, Wei Tang

“…A 2 cm water depth had no significant effect on growth, while a 4 cm water depth completely inhibited plant height and aboveground biomass accumulation. …”
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Single-cell spatial transcriptomics unravels cell states and ecosystems associated with clinical response to immunotherapy by Sjoerd H van der Burg, Ziena Abdulrahman, Mariette I E van Poelgeest, Roderick C Slieker, Marij J P Welters, Daniel McGuire

“…We leveraged single-cell spatial transcriptomics to systematically dissect the intricate complexity of the TME, in particular the cellular heterogeneity and spatial interactions. …”
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Transcriptomics Revealed Differentially Expressed Transcription Factors and MicroRNAs in Human Diabetic Foot Ulcers by Vikrant Rai

“…The ongoing research based on proteomics and transcriptomics has predicted multiple potential targets, but there is no definitive therapy to enhance healing in chronic DFUs. …”
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