Integrated Single-Cell and Spatial Transcriptomic Analysis Identifies ISR-Related Genes Driving Immune Regulation in Parkinson’s Disease by Jiang H, Zhang X, Feng S, Feng W

“…CIBERSORT was applied to assess immune cell infiltration, while spatial transcriptomics mapped the regional expression of key genes. …”
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Metabolome and transcriptomics analyses reveal quality differences between Camellia tachangensis F. C. Zhang and C. sinensis (L.) O. Kunzte. by Yunfei Xu, Qihang Zhou, Xinglin Wang, Xingpan Meng, Zhengdong Zhang, Xu Zhang, Ximin Zhang, Suzhen Niu, Guiping Chen, Lunxian Liu, Tie Shen

“…Additionally, transcriptome analysis revealed 8049 differentially expressed genes, with 4418 upregulated and 3631 downregulated genes. …”
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2-Hydroxy-4-methoxybenzaldehyde (HMB) disrupts ergosterol biosynthesis, redox metabolism, and DON biosynthesis of Fusarium graminearum revealed by transcriptome analysis by Hongying Xiao, Yiming Zhang, Qian Li

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Integrated Transcriptome and Metabolome Analysis Revealed Mechanism Underlying Anthocyanin Biosynthesis During Flower Color Formation in <i>Lagerstroemia indica</i> by Zilong Gao, Zhuomei Chen, Jinfeng Wang, Weixin Liu

“…<i>Lagerstroemia indica</i> is a widely used ornamental woody plant known for its summer flowering and significant ornamental and economic value. While <i>L. indica</i> boasts a variety of rich flower colors, the molecular mechanisms underlying this color formation remain unclear. …”
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Integrated Metabolomic and Transcriptomic Analysis of Volatile Organic Compound Biosynthesis During Mung Bean (<i>Vigna radiata</i>) Seed Development by Nan Xiang, Yihan Zhao, Bing Zhang, Honglin Chen, Xinbo Guo

“…This study investigated the VOC and flavor composition in four mung bean varieties by integrating relative odor activity value (ROAV) evaluation and transcriptomic analysis. A total of 65 VOCs were identified, with eucalyptol serving as a key maturity indicator in LL655 and SH-1, while nonanal contributed significantly to the characteristic beany flavor across all varieties. …”
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A Transcriptomic Study on the Toxic Effects of Iodide (I⁻) Wet Deposition on Pepper (<i>Capsicum annuum</i>) Leaves by Rui Yu, Zhu-Ling Ma, Min Wang, Jie Jin

“…Using sodium iodide (NaI) as the exposure agent, transcriptomic analysis was conducted to evaluate the molecular responses of chili pepper leaves to iodine at concentrations of 2, 4, and 8 ppm. …”
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Transcriptome of <i>Arabidopsis thaliana</i> Plants Exposed to Human Parasites <i>Cryptosporidium parvum</i> and <i>Giardia lamblia</i> by Yaroslav Ilnytskyy, Andrey Golubov, Boseon Byeon, Igor Kovalchuk

“…Previous work demonstrates that animal pathogenic bacteria can be recognized by plant receptors and alter transcriptome. In this work, we have hypothesized that exposure to human parasites, <i>Cryptosporidium parvum</i> and <i>Giardia lamblia</i>, would also trigger pathogen response in plants, leading to changes in transcriptome. …”
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Comprehensive Transcriptomic Analysis of <i>Spodoptera frugiperda</i> Reveals Stage-Specific Gene Expression and P450-Mediated Adaptation Mechanisms by Ziqi Cheng, Zhe Huang, Bin Yan, Xing Huang, Yang Mei

“…Functional enrichment revealed that the sixth instar stage prioritizes pathways related to growth and tissue remodeling, while adult males emphasize reproductive and sensory functions. …”
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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

“…Compared to normal meat, WB meat demonstrated moderate molecular changes, while WS meat showed minimal transcriptomic impact. …”
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Dietary Cholesterol Supplementation Inhibits the Steroid Biosynthesis but Does Not Affect the Cholesterol Transport in Two Marine Teleosts: A Hepatic Transcriptome Study by Ziling Song, Haiyan Xiong, Xiaoxue Meng, Qiang Ma, Yuliang Wei, Yanlu Li, Jian Liu, Mengqing Liang, Houguo Xu

“…The control diet contained 30% fish meal (0% fish oil) without cholesterol supplementation, while the treatment diet was supplemented with 1.0% cholesterol (CHO-1.0). …”
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Identification of novel androgen-regulated pathways and mRNA isoforms through genome-wide exon-specific profiling of the LNCaP transcriptome. by Prabhakar Rajan, Caroline Dalgliesh, Phillippa J Carling, Thomas Buist, Chaolin Zhang, Sushma N Grellscheid, Kelly Armstrong, Jacqueline Stockley, Cedric Simillion, Luke Gaughan, Gabriela Kalna, Michael Q Zhang, Craig N Robson, Hing Y Leung, David J Elliott

“…Although several microarray-based studies have identified androgen-regulated genes, here we identify in-parallel global androgen-dependent changes in both gene and alternative mRNA isoform expression by exon-level analyses of the LNCaP transcriptome. While genome-wide gene expression changes correlated well with previously-published studies, we additionally uncovered a subset of 226 novel androgen-regulated genes. …”
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Identification and validation of m6A RNA methylation and ferroptosis-related biomarkers in sepsis: transcriptome combined with single-cell RNA sequencing by Jinshuai Lu, Jianhao Wang, Kun Han, Yuxia Tao, Jiyi Dong, Xiaoyu Pan, Xiaolan Wen

“…BackgroundSepsis, a systemic inflammatory response syndrome triggered by infection, is associated with high mortality rates and an increasing global incidence. While N6-methyladenosine (m6A) RNA methylation and ferroptosis are implicated in inflammatory diseases, their specific genes and mechanisms in sepsis remain unclear.MethodsTranscriptomic datasets of sepsis, along with m6A-related genes (m6A-RGs) and ferroptosis-related genes (FRGs), were sourced from public databases. …”
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Comprehensive GWAS and Transcriptome Analysis Discovered Candidate Gene Associated with Starch Pasting Properties of Temperate japonica rice (Oryza sativa L.) by Yoon Kyung Lee, Su Jang, Jihwan Im, Hee-Jong Koh

“…LD block analysis and transcriptome analysis of accessions with extreme phenotypes identified OsGLUTN (Os02g0224300/LOC_Os02g13130), a gene encoding a high molecular weight glutenin subunit-like protein, as a strong candidate. …”
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Integrated transcriptome and metabolome analyses reveals the mechanisms of function loss of Lr29 leaf rust resistance gene at high temperatures in wheat by Liwen Wang, Yang Yu, Hang Li, Mingzhu Lu, Shubo Cao, Ziqi Li, Haoyuan Song, Laszlo Purnhauser, Jinlong Li, Jiajie Wu

“…We also found that, at high temperatures, Lr29 downregulated the genes and metabolites associated with glycolysis and the tricarboxylic acid (TCA) cycle, while genes and metabolites related to the shikimic acid pathway were upregulated. …”
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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

“…A total of 16 lung cancer tissue samples were collected from a cohort of 12 NSCLC patients and subjected to single-cell RNA and spatial transcriptome sequencing. Our data demonstrated that the distribution of CD4 + Treg T cells and mCAFs indicated an immunosuppressive tumor microenvironment, while the accumulation of CD4 + Th17 T cells and iCAFs could act as a positive marker for the sensitivity to chemoimmunotherapy. …”
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Single-cell sequencing and transcriptomic data reveal that P65 activation significantly promotes microglia-mediated neuroinflammation after ischemic stroke by Ruiyu Wang, Yilun Qian, Xinchen Zhou, Hang Xu, Yu Wang, Yao Geng, Tianshu Wang, Binxiu Sha

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Integrated Transcriptomic, Proteomic, and Metabolomic Analyses Reveal Mechanisms Underlying Day–Night Differences in Carbohydrate Metabolism between Diploid and Tetraploid Rice by Weilong Meng, Yuchen Liu, Changjiang Zhang, Xiaohong Zhan, Yingkai Wang, Xinfang Yu, Chunying Zhang, Ningning Wang, Jian Ma

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Inference of cell type content from human brain transcriptomic datasets illuminates the effects of age, manner of death, dissection, and psychiatric diagnosis. by Megan Hastings Hagenauer, Anton Schulmann, Jun Z Li, Marquis P Vawter, David M Walsh, Robert C Thompson, Cortney A Turner, William E Bunney, Richard M Myers, Jack D Barchas, Alan F Schatzberg, Stanley J Watson, Huda Akil

“…We conclude that accounting for cell type can greatly improve the interpretability of transcriptomic data.…”
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Multi-omics integration reveals chromatin-associated lncRNA prognostic model in lung adenocarcinoma: Bridging GWAS, transcriptome and clinical outcomes by Xiao Zhu, Zhuolong Xiong

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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

“…Conversely, ML 125-2 displayed total soluble protein content and SPA similar to IS21, while chlorophyll and proline content were not significantly different from those of MR220. …”
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