Isolation and characterization of Lentilactobacillus diolivorans: a high n-propanol-producing microorganism from Baijiu brewing by Enhua Zhang, Ruijie Gao, Kai Zhu, Pulin Liu, Weifang Liao, Tuanyuan Yang, Xiaotong Liang, Menglu Yang, Yingying Ming, Lihong Miao

“…High n-propanol synthesis from L. diolivorans ZX6 required high sugar concentrations, anaerobic conditions, and extended fermentation times. Transcriptome analysis revealed that pyruvate and lactic acid, likely major precursors, could enter the methylglyoxal pathway under the catalysis of lactaldehyde dehydrogenase, respectively. …”
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Functional validation to explore the protective role of miR-223 in Staphylococcus aureus-induced bovine mastitis by Xueqin Liu, Siyuan Mi, Gerile Dari, Siqian Chen, Jiuzhou Song, David E. MacHugh, Ying Yu

“…These genes were significantly enriched in QTL regions associated with bovine mastitis resistance, underscoring their relevance in genetic regulation of disease resilience. Our findings provide critical genetic markers for enhancing mastitis resistance, particularly S. aureus-induced mastitis, through selective breeding. …”
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Allelic expression patterns of imprinted and non-imprinted genes in cancer cell lines from multiple histologies by Julia Krushkal, Travis L. Jensen, George Wright, Yingdong Zhao

“…We also identified additional genes and isoforms with predominantly monoallelic expression due to a variety of potential mechanisms. We provide a novel public dataset of transcriptome-wide allelic expression patterns in cell lines from diverse tumor categories, which can serve as a resource for future cancer studies. …”
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Analyzation of the Peripheral Blood Mononuclear Cells Atlas and Cell Communication of Rheumatoid Arthritis Patients Based on Single-Cell RNA-Seq by Xinqiang Song, Yu Zhang, Lijun Zhao, Jinke Fan, Tao Peng, Ying Ma, Nailiang Guo, Xiaotong Wang, Xudong Liu, Zhe Liu, Lei Wang

“…ScRNA-seq was performed on four RA samples and integrated with single-cell transcriptome data from four healthy control samples downloaded from publicly available databases for analysis. …”
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The role of CD47 in immune escape of colon cancer and its correlation with heterogeneity of tumor immune microenvironment by Qiu-Si Tian, ChunMei Zhang, Zhi-Jun Bao, ZhiGang Pei

“…To explore the association between CD47 expression and clinicopathological characteristics, we integrated transcriptome data from The Cancer Genome Atlas and the Gene Expression Omnibus using R software. …”
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Combined Analysis of BSA-Seq and RNA-Seq Reveals Candidate Genes for <i>qGS1</i> Related to Sorghum Grain Size by Qi Shen, Kai Wang, Lu Hu, Lei Li, Lihua Wang, Yongfei Wang, Yi-Hong Wang, Jieqin Li

“…The expression and bioinformatics analysis showed Sobic.001G230700 was the most likely candidate gene for the qGS1 locus. This study provides new insights into the genetic regulation of grain size and a new target to improve grain size in sorghum.…”
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A Novel Molecular Classification Method for Glioblastoma Based on Tumor Cell Differentiation Trajectories by Guanghao Zhang, Xiaolong Xu, Luojiang Zhu, Sisi Li, Rundong Chen, Nan Lv, Zifu Li, Jing Wang, Qiang Li, Wang Zhou, Pengfei Yang, Jianmin Liu

“…Although differentiation trajectory inference based on single-cell sequencing (scRNA-seq) data holds great promise for identifying cell heterogeneity, it has not been used in the study of GBM molecular classification. Single-cell transcriptome sequencing data from 10 GBM samples were used to identify molecular classification based on differentiation trajectories. …”
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Mechanisms of skeletal muscle atrophy in type 2 diabetes mellitus by Jingyi Yang, Yingdong Wang, Yuzhe Xu, Xinqi Jia, Fangping Lu

“…Pathway enrichment analysis of differentially expressed genes was performed based on transcriptome sequencing data, focusing on apoptosis, ERS, and ubiquitin-proteasome pathways. …”
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Dyrk1a Phosphorylation of α-Synuclein Mediating Apoptosis of Dopaminergic Neurons in Parkinson’s Disease by Yuxuan Yong, Qinfen Wu, Xinling Meng, Ranran Lu, Huan Xia, Feifei Pei, Xinling Yang

“…Abnormal Dyrk1a expression can affect α-synuclein phosphorylation modifications, and dyrk1a knockdown activates the PI3K/AKT pathway and reduces dopaminergic neuron apoptosis. It provides a theoretical basis for the group to further investigate the molecular mechanism.…”
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Genome-wide identification of starch metabolism gene families in Potentilla anserina and the expression pattern in response to abiotic stress factors by Yangmiao Jiao, Qin He, Xu Li, Yang Chen, Tingting Tian, Liang Cao, Zaiqi Zhang

“…An overview of evolution of AMY and BAM gene families within rosids was also provided.…”
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Identification of the Plant Defensin (MsPDF) Gene Family in <i>Medicago sativa</i> and Analysis of Expression Patterns Under Abiotic Stress by Meiyan Guo, Xiuhua Chen, Shuaixian Li, Jiang Tian, Wangqi Huang, Yongjun Shu

“…This study lays the foundation for the identification and evolutionary relationship analysis of the MsPDF gene family, and provides a new reference for subsequent research on abiotic stress resistance.…”
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Decoding regulatory programs underlying placode and dermal condensate cell fate commitment during hair follicle induction via single‐cell multi‐omics analysis by Fang Li, Minghao Li, Tongtong Zhang, Menghua Sui, Hasan Khatib, Xin Wang

“…To identify cell‐type‐specific chromatin accessibility patterns in the developing HF, we integrated chromatin accessibility and transcriptome profiles at single‐cell resolution during the murine HF induction stage. …”
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Hydrogen-Releasing Micromaterial Dressings: Promoting Wound Healing by Modulating Extracellular Matrix Accumulation Through Wnt/β-Catenin and TGF-β/Smad Pathways by Pengxiang Zhao, Yufei Li, Boyuan Guo, Ziyi Liu, Xujuan Zhang, Mengyu Liu, Xuemei Ma

“…<b>Conclusions</b>: Overall, these results provide a novel insight into the field of hydrogen treatment and wound healing.…”
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Genome-Wide Characterization, Evolution and Expression Profiling of the UDP-Glycosyltransferase Family in Grapes (Vitis vinifera) by WANG Yuanyuan, LIU Yunqing, XU Jingyu, LIU Yunting, HU Xixi, ZHANG Chao, JIANG Zeyu, ZHU Lei

“…Anthocyanin contents and glycosylated anthocyanin composition were significantly different among the three grape varieties. Transcriptome analysis showed that the expression patterns of 85 VvUGT genes with high expression levels during the veraison process showed significant differences between varieties and growth periods. …”
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Transcriptional profiling of Chlamydia trachomatis and its host in an ex vivo endocervical primary cell culture system using dual RNA sequencing by Olusola Olagoke, Siddharth Chittaranjan, Deborah Dean, Deborah Dean, Deborah Dean, Deborah Dean, Deborah Dean

“…Understanding host-pathogen interactions is challenging but dual RNA sequencing offers simultaneous transcriptome data for comprehensive interrogations into these interactions. …”
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Deep sequencing reveals distinct microRNA-mRNA signatures that differentiate pancreatic neuroendocrine tumor from non-diseased pancreas tissue by N Matyasovska, N Valkova, M Gala, S Bendikova, A Abdulhamed, V. Palicka, Neil Renwick, Pavol Čekan, Evan Paul

“…Abstract Background Only a limited number of biomarkers guide personalized management of pancreatic neuroendocrine tumors (PanNETs). Transcriptome profiling of microRNA (miRs) and mRNA has shown value in segregating PanNETs and identifying patients more likely to respond to treatment. …”
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The transcriptional response to yellow and wilt disease, caused by race 6 of Fusarium oxysporum f. sp. Ciceris in two contrasting chickpea cultivars by Aliakbar Faramarzpour, Sara Dezhsetan, Hamid Hassaneian Khoshro, Raheleh Mirdar Mansuri, Hamid Reza Pouralibaba, Zahra-Sadat Shobbar

“…Results To identify genes and pathways involved in resistance to race 6 of Foc, this study utilized transcriptome sequencing of two chickpea cultivars: resistant (Ana) and susceptible (Hashem) to Foc race 6. …”
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Identification and Expression Analysis of the <i>bHLH</i> Gene Family in <i>Rhododendron</i> × <i>pulchrum</i> Sweet with Different Flower Colors by Jiaran Sheng, Jianshang Shen, Yingying Shan, Xia Chen, Xueqin Li, Huasen Wang, Songheng Jin

“…This study will enhance our understanding of <i>RpbHLH</i> functions and provide a reference for the study of flower development and coloration in <i>R</i>. …”
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Expression of regulatory platelet microRNAs in patients with sickle cell disease. by Shilpa Jain, Maria G Kapetanaki, Nalini Raghavachari, Kimberly Woodhouse, Guoying Yu, Suchitra Barge, Claudia Coronnello, Panayiotis V Benos, Gregory J Kato, Naftali Kaminski, Mark T Gladwin

“…The role for post-transcriptional regulation of the platelet transcriptome by microRNAs (miRNAs) in SCD has not been previously explored. …”
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Expression patterns and clinical significance of vasculogenic mimicry-related genes in patients with head and neck squamous cell carcinoma by Rui Lai, Xuanyu Gu, Yueyue Cai, Qiang Li

“…Cox regression and ROC analyses showed that the risk model provided independent and robust predictive value for the prospects of individuals with HNSCC. …”
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