An integrated machine learning model of transcriptomic genes in multi-center chronic obstructive pulmonary disease reveals the causal role of TIMP4 in airway epithelial cell by Erkang Yi, Haiqing Li, Yu Liu, Qingyang Li, Chengshu Xie, Ruining Sun, Fan Wu, Zhishan Deng, Kunning Zhou, Hairong Wang, Xinru Ran, Yumin Zhou, Pixin Ran

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Heterogenous cancer-associated fibroblasts related tumor microenvironment marked by CD10/KLF4/TIAM1 were identified in pancreatic adenocarcinoma by integrated transcriptomics by Yu Wan, Yu Wan, Yu Wan, Qiong Hu, Kai Sun, Jing Shi, Limei Liu, Xiangsong Zhang, Jianjun Huang, Chulan Gong, Jinting Liu, Haijiu Wang, Jun Yan, Jun Yan

“…By utilizing multiplex immunohistochemistry and spatial transcriptomics, we also identified key CAF subpopulations, such as iCAF_17, iCAF_19, and myCAF_12, which were found to interact closely with tumor cells and macrophages. …”
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Unveiling Stage-Specific Flavonoid Dynamics Underlying Drought Tolerance in Sweet Potato (<i>Ipomoea batatas</i> L.) via Integrative Transcriptomic and Metabolomic Analyses by Tao Yin, Chaoyu Song, Huan Li, Shaoxia Wang, Wenliang Wei, Jie Meng, Qing Liu

“…Transcriptome analysis identified 8292 and 13,509 differentially expressed genes in DS1 and DS2, respectively, compared with the well-watered control (75 ± 5% field capacity). …”
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Comparative Transcriptome Analysis Reveals the Mechanism by Ethylene and 1-Methylcyclopropene Treatment on the Vase Life of Cut <i>Oncidium hybridum</i> ‘<i>Honey Angle</i>’ by Jingjing Kou, Xueqian Zang, Zirui Mo, Guangwei Wu, Bei Wang, Guopeng Zhu

“…The petal changes, vase life, and transcriptomic analysis after treatments were investigated. …”
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Seed coat transcriptomic profiling of 5-593, a genotype important for genetic studies of seed coat color and patterning in common bean (Phaseolus vulgaris L.) by Jayanta Roy, Avinash Sreedasyam, Caroline Osborne, Rian Lee, Phillip E. McClean

“…Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that phenylpropanoid biosynthesis, flavonoid biosynthesis, and plant hormone signal transduction comprised the principal pathways expressed during bean seed coat pigment development. Transcriptome analysis suggested that most structural genes for flavonoid biosynthesis and some potential regulatory genes were significantly differentially expressed. …”
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Identification of key genes involved in collagen hydrogel-induced chondrogenic differentiation of mesenchymal stem cells through transcriptome analysis: the role of m6A modificatio... by Chaotao Chen, Kai Xiong, Kanglu Li, Bo Zhou, Jianwen Cheng, Bo Zhu, Li Zheng, Jinmin Zhao

“…In conclusion, our study provides valuable insights into the molecular mechanisms of collagen hydrogel-induced chondrogenic differentiation of BMSCs, which may aid in developing more effective strategies for cartilage regeneration. …”
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Transcriptomic analysis of the interactions between Fibrobacter succinogenes S85, Selenomonas ruminantium PC18 and a live yeast strain used as a ruminant feed additive by Pauline Desvignes, Philippe Ruiz, Laurie Guillot, Jeanne Danon, Alexandra Durand, Martin Beaumont, Frédérique Chaucheyras-Durand, Evelyne Forano

“…Interactions were studied through RNA-seq transcriptomic analysis of various microbial combinations, alongside substrate consumption and metabolite production measurements. …”
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Genome-Wide Association Integrating a Transcriptomic Meta-Analysis Suggests That Genes Related to Fat Deposition and Muscle Development Are Closely Associated with Growth in Huaxi... by Cheng-Li Liu, Tao Ren, Peng-Cheng Ruan, Yong-Fu Huang, Simone Ceccobelli, De-Jun Huang, Lu-Pei Zhang, Guang-Xin E

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Comparative transcriptomic analysis of Rosa sterilis inflorescence branches with different trichome types reveals an R3-MYB transcription factor that negatively regulates trichome... by Wen-tao MA, Min LU, Hua-ming AN, Yin YI

“…Comparative transcriptomic analysis showed that many transcription factors (TFs) are potentially involved in the formation and development of trichomes. …”
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Transcriptomic Analysis Reveals That the Photosynthesis and Carotenoid Metabolism Pathway Is Involved in the Salinity Stress Response in <i>Brassica rapa</i> L. ssp. <i>Pekinensis<... by Jin Jia, Fengshuo Wang, Mengmeng Yuan, Zhiying Wang, Zhe Qin, Xiaoli Zhang, Yutao Shao, Haixia Pei

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Comprehensive single-cell transcriptomic reveals different destinies of melanocytes and dynamic changes of immune microenvironment in a psychological stress-induced leukoderma and... by Xuechen Cao, Yongkai Yu, Hang Yao, Yujie Zheng, Jiawei Lu, Yifei Feng, Tongxin Pei, Ziyu Li, Ming Lu, Yan Lu

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Novel insights into the Leishmania infantum transcriptome diversity of protein-coding and non-coding sequences in both stages of parasite development using nanopore direct RNA sequ... by Jean-Guillaume Emond-Rheault, Gabriel Reis Ferreira, Camille Lavoie-Ouellet, Martin A. Smith, Barbara Papadopoulou

“…Our findings advance knowledge on existing Leishmania expression datasets and provide new insights into the transcriptome complexity and dynamics of both protein-coding and non-coding sequences throughout the parasite development.…”
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Transcriptome analysis of the early maturity mechanism of the rice cultivar ‘Yongxian 15’(基于转录组的水稻‘甬籼15’早熟机制解析) by 张雨洁(ZHANG Yujie), 杨繁婧(YANG Fanjing), 应泉盛(YING Quansheng), 姜洁锋(JIANG Jiefeng), 叶楚玉(YE Chuyu), 施贤波(SHI Xianbo)

“…In this study, we conducted a series of transcriptome analyses on ‘Yongxian 15’ (early-maturing) and ‘Zhongzao 39’ (medium-maturing) during critical stages of spikelet differentiation. …”
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Comparative transcriptome reveals genes regulating root hair length of barley(基于比较转录组发掘控制大麦根毛长度的基因) by 贺小彦(HE Xiaoyan), 王永梅(WANG Yongmei), 何东(HE Dong), 吴港(WU Gang), 孙庆译(SUN Qingyi), 孙雪莲(SUN Xuelian), 刘文星(LIU Wenxing), 曾建斌(ZENG Jianbin)

“…In this study, by analyzing the transcriptome of barley roots which exhibiting significant differences in root hair length, we identified 274 shared differentially expressed genes. …”
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Contrasting gene expression patterns during floral induction in two Chenopodium ficifolium genotypes reveal putative flowering regulators by David Gutiérrez-Larruscain, Manuela Krüger, Oushadee A. J. Abeyawardana, Claudia Belz, Petre I. Dobrev, Radomíra Vaňková, Kateřina Eliášová, Zuzana Vondráková, Miloslav Juříček, Helena Štorchová

“…Owing to its reproducible germination and seedling development, it becomes a promising model for studying floral induction, providing a basis for the comparison with C. quinoa. …”
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Immunotranscriptomic Profiling of <i>Spodoptera frugiperda</i> Challenged by Different Pathogenic Microorganisms by Yan Tang, Qi Zou, Guojie Yu, Feng Liu, Yu Wu, Xueyan Zhao, Wensheng Wang, Xinchang Liu, Fei Hu, Zengxia Wang

“…This study elucidates the immune transcriptome of <i>S. frugiperda</i> in response to various pathogenic microorganisms, providing valuable insights for improving the effectiveness of existing microbial agents and developing new, highly efficient, and specific biopesticides.…”
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Evaluation of reference genes for gene expression analysis in Japanese flounder (Paralichthys olivaceus) under temperature stress by Ping Han, Jianming Chen, Zhennan Sun, Shengjie Ren, Xubo Wang

“…Conclusion This study transcriptome-wide identified reference genes in different tissues of Japanese flounder exposed to temperature stress for the first time, providing a basis for gene expression research in flatfish.…”
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De novo transcriptome assembly of Aureobasidium melanogenum CGMCC18996 to analyze the β-poly(L-malic acid) biosynthesis pathway under the CaCO3 addition by Genan Wang, Haisong Yin, Tingbin Zhao, Donglin Yang, Shiru Jia, Changsheng Qiao

“…In this study, we sequenced the transcriptome of strain Aureobasidium melanogenum under 20 g/L CaCO3 addition. …”
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Novel Clinical Insights into the Pathogenesis of Posttraumatic Elbow Stiffness: An Expression Profile Analysis of Contracted Joint Capsule in Human by Liu N, Dong J, Li L, Xu J, Yang C, Yu Z, Liu F

“…This study aims to identify differentially expressed genes (DEGs) and elucidate molecular networks of posttraumatic elbow stiffness, providing novel insights into disease mechanisms at transcriptome level.Methods: Global transcriptome sequencing was conducted on six capsular samples from individuals with posttraumatic elbow stiffness and three control capsular samples from individuals with elbow fractures. …”
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Convergent and divergent transcriptional reprogramming of motor and sensory neurons underlying response to peripheral nerve injury by Jian Yang, Shuqiang Zhang, Xiaodi Li, Zhifeng Chen, Jie Xu, Jing Chen, Ya Tan, Guicai Li, Bin Yu, Xiaosong Gu, Lian Xu

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