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 landscape of atherosclerotic plaque progression: insights from proteomics, single-cell transcriptomics and genomics by Chaonan Wang, Yuyao Feng, Xiaoyan Liu, Haidan Sun, Zhengguang Guo, Jiang Shao, Kang Li, Junye Chen, Keqiang Shu, Deqiang Kong, Jiaxian Wang, Yiran Li, Xiangling Lei, Chen Li, Bao Liu, Wei Sun, Zhichao Lai

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Transcriptomic and electrophysiological alterations underlying phenotypic variability in SCN1A-associated febrile seizures by Stefania Scalise, Alessandro Gaeta, Elio Aprigliano, Valeria Lucchino, Raffaele Covello, Mariagrazia Talarico, Barbara Puccio, Pietro Hiram Guzzi, Pierangelo Veltri, Antonio Gambardella, Lilian Juliana Lissner, Alessandra Morano, Pierangelo Cifelli, Veronica Alfano, Eleonora Palma, Gerardo Perozziello, Gabriele Ruffolo, Giovanni Cuda, Elvira Immacolata Parrotta

“…Despite sharing the mutation, only the older sibling developed temporal lobe epilepsy (TLE). Transcriptomic analysis revealed downregulation of GABAergic pathway genes in both siblings’ neurons, aligning with SCN1A-associated epilepsy. …”
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Spatial transcriptomics reveals substantial heterogeneity in triple-negative breast cancer with potential clinical implications by Xiaoxiao Wang, David Venet, Frédéric Lifrange, Denis Larsimont, Mattia Rediti, Linnea Stenbeck, Floriane Dupont, Ghizlane Rouas, Andrea Joaquin Garcia, Ligia Craciun, Laurence Buisseret, Michail Ignatiadis, Marcela Carausu, Nayanika Bhalla, Yuvarani Masarapu, Eva Gracia Villacampa, Lovisa Franzén, Sami Saarenpää, Linda Kvastad, Kim Thrane, Joakim Lundeberg, Françoise Rothé, Christos Sotiriou

“…Abstract While triple-negative breast cancer (TNBC) is known to be heterogeneous at the genomic and transcriptomic levels, spatial information on tumor organization and cell composition is still lacking. …”
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Multi-omic insights into mitochondrial dysfunction and prostatic disease: evidence from transcriptomics, proteomics, and methylomics by Binbin Gong, Binbin Gong, Binbin Gong, Feixiang Yang, Feixiang Yang, Feixiang Yang, Ning Zhang, Zhengyang Wu, Tianrui Liu, Kun Wang, Xiangyu Zhang, Yangyang Zhang, Zhengyao Song, Chaozhao Liang, Chaozhao Liang, Chaozhao Liang

“…BackgroundProstatic diseases, consisting of prostatitis, benign prostatic hyperplasia (BPH), and prostate cancer (PCa), pose significant health challenges. While single-omics studies have provided valuable insights into the role of mitochondrial dysfunction in prostatic diseases, integrating multi-omics approaches is essential for uncovering disease mechanisms and identifying therapeutic targets.MethodsA genome-wide meta-analysis was conducted for prostatic diseases using the genome-wide association studies (GWAS) data from FinnGen and UK Biobank. …”
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Differences in the pathological, transcriptomic, and prognostic implications of lymphoid structures between primary and metastatic cutaneous melanomas by Jin Xu, Andrew Knight, Jonathan Nguyen, Hong Wang, Walter J Storkus, Cindy Sander, John M Kirkwood, Jiqiang Yao, Xiaofei Song, Jane Messina, James J Mulé, Lilit Karapetyan, Carlos Moran-Segura, Aofei Li, Marion Joy, Sabrina Bruno, Hassan M Abushukair, Danielle Vargas De Stefano, Ayah N Al-Bzour, Caroline Layding

“…Background While the prognostic role of tertiary lymphoid structures (TLS) has been well studied in solid cancers, the prevalence and impact of immature precursor lymphoid structures known as lymphoid aggregates (LA) remain unresolved in relation to the disease process. …”
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mNSF: multi-sample non-negative spatial factorization by Yi Wang, Kyla Woyshner, Chaichontat Sriworarat, Genevieve Stein-O’Brien, Loyal A. Goff, Kasper D. Hansen

“…Through simulations and real data analysis, we demonstrate mNSF’s efficacy in identifying true factors, shared anatomical regions, and region-specific biological functions. mNSF’s performance is comparable to alignment-based methods when alignment is feasible, while enabling analysis in scenarios where spatial alignment is unfeasible. mNSF shows promise as a robust method for analyzing spatially resolved transcriptomics data across multiple samples.…”
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Short- and Long-Term Endothelial Inflammation Have Distinct Effects and Overlap with Signatures of Cellular Senescence by Barbora Belakova, José Basílio, Manuel Campos-Medina, Anna F. P. Sommer, Adrianna Gielecińska, Ulrike Resch, Johannes A. Schmid

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Characterization of canine tumor-infiltrating leukocyte transcriptomic signatures reveals conserved expression patterns with human osteosarcoma by Dylan T. Ammons, R. Adam Harris, Lyndah Chow, Steven Dow

“…Comparisons to human literature and analysis of human scRNA-seq data revealed conserved transcriptomic responses to tumor infiltration, while also identifying species differences. …”
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A cross‐tissue transcriptome‐wide association study identifies novel susceptibility genes for atrial fibrillation by Yalin Yuan, Xin Zheng, Wenjing Zhang, Zhaoyu Ren, Bin Liang

“…Elevated expression of FKBP7, CEP68, and CAMK2D increases AF risk, while SPATS2L showed a protective effect, with colocalization analysis implicating CEP68 and SPATS2L as prioritized candidates. …”
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Transcriptome and hormones metabolome joint analyses reveal the key molecular mechanism of Sweetpotato storage roots sprouting by Fan Ding, Xue Zou, Heling Fan, Li-ping Rao, Jian Sun, Qiang Li

“…Both GO analysis and KEGG analysis indicated that DEGs in strong-sprouting variety (0d_vs_3d) were primarily related to photosynthesis. …”
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Integration of transcriptome and Mendelian randomization analyses in exploring the extracellular vesicle-related biomarkers of diabetic kidney disease by Xu Yang, Rensong Yue, Liangbin Zhao, Qiyue Wang

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Novel insights into the genetic basis and transcriptomic elucidation of virulence attenuation in Pseudomonas syringae pv. actinidiae variants by Muhammad Asif, Renjian Hu, Ting Xie, Rong Fan, Youhua Long, Yong Wang, Shiping Wu, Zhibo Zhao, Lili Huang

“…Transcriptomic analysis showed widespread alterations in key aspects of the secretion system, protein transport, and signal transduction, further supporting the phenotype characteristics exhibited by the strains. …”
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Transcriptome and Cellular Evidence of Depot-Specific Function in Beef Cattle Intramuscular, Subcutaneous, and Visceral Adipose Tissues by Alexandra P. Tegeler, Hunter R. Ford, Jean Franco Fiallo-Diez, Tainara C. Michelotti, Bradley J. Johnson, Oscar J. Benitez, Dale R. Woerner, Clarissa Strieder-Barboza

“…IMAT. Functional transcriptome analysis demonstrated the activation of pathways for lipid metabolic processes and biosynthesis in SCAT, accompanied by increased preadipocyte proliferation, adipocyte size, and insulin responses of SCAT in vitro. …”
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Combining Transcriptome and Hormone-Targeted Metabolome Analyses to Dissect the Regulatory Mechanisms Underlying Wheat Peduncle Elongation by Huifang Hao, Lu Chen, Zhiyang Cao, Xiujuan Jin, Feng Guo, Zerui Shi, Jinwen Yang, Juan Lu, Daizhen Sun

“…We conducted phenotypic identification, genetic analysis, and cytological observation combined with transcriptome and targeted hormone metabolism analysis and compared the differences between the <i>eui</i> mutant and the wild-type (WT). …”
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In-Depth Exploration of the Coloration Mechanism of <i>Iris dichotoma</i> Pall. via Transcriptomic and Metabolomic Analyses by Yalin Yu, Xiaojing Qiang, Fan Huang, Xiuzheng Huang, Lei Liu

“…A comprehensive integrative analysis of the transcriptome and metabolome of the two petal types was carried out. …”
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Enhancing growth performance in Liangshan black sheep through fermented onion: insights from transcriptomics and metabolomics by Chaoyun Yang, Shuzhe Wang, Yunxia Qi, Yadong Jin, Ran Guan, Zengwen Huang

“…Rumen epithelial tissue was then collected for transcriptome sequencing, while fermented and unfermented onions were collected for untargeted metabolomics. …”
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Transcriptome and Metabolome Analyses Reveal High-Altitude Adaptation Mechanism of Epididymis Sperm Maturation in Tibetan Sheep by Yijian Li, Yanan Yang, Binyan Yu, Rong Gao, Xinrong Wang

“…Transcriptomic analysis revealed 139 differentially expressed genes in the Tibetan sheep epididymis under high-altitude conditions. …”
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Spatial transcriptomics and scRNA-seq: decoding tumor complexity and constructing prognostic models in colorectal cancer by Wei Song, Yatao Wang, Min Zhou, Fengqin Guo, Yanliang Liu

“…Abstract Introduction Recent advancements in transcriptomic analysis, combined with single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics, have deepened our understanding of the tumor microenvironment and cellular heterogeneity, laying the groundwork for personalized therapies. …”
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Integrative transcriptomics and metabolomics reveal neuroendocrine-lipid crosstalk and adenosine signaling in broiler under heat stress by Bingxing An, Peihao Liu, Zhirui Yang, Fan Ying, Dawei Liu, Jie Wen, Guiping Zhao

“…Then, the comparative transcriptome analysis of the hypothalamus and pituitary revealed 358 differentially expressed genes (DEGs), highlighting tissue-specific adaptive pattern. …”
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