Transcriptome analysis reveals defense responses of alfalfa seedling roots to Sclerotium rolfsii by Shizhen Jia, Shizhen Jia, Zhencuo Dan, Zhencuo Dan, He Li, He Li, Yuhan Guo, Yuhan Guo, Lei Jia, Lei Jia, Ailing Yu, Ailing Yu, Huitong Zhan, Huitong Zhan, Xiangjun Liu, Xiangjun Liu, Teng Gao, Teng Gao, Yun Shi, Yun Shi, Zeng-Yu Wang, Zeng-Yu Wang, Lili Cong, Lili Cong, Lili Cong

“…This study aims to explore the interaction mechanisms between alfalfa and S. rolfsii, identify key regulatory factors involved in disease resistance, and provide insights for improving alfalfa's resistance to root rot. …”
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Transcriptome Analysis of Low-Temperature-Induced Breaking of Garlic Aerial Bulb Dormancy by Yuhui Dong, Mengjiao Guan, Lixia Wang, Lei Yuan, Xiudong Sun, Shiqi Liu

“…The high-throughput transcriptome sequencing results showed that 6,675 DEGs were upregulated and 36,596 DEGs were downregulated in the aerial bulbs given low-temperature treatment. …”
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Transcriptome Analysis of Dimethyl Fumarate Inhibiting the Growth of <i>Aspergillus carbonarius</i> by Siruo Wang, Bowen Tai, Xifan Yu, Erfeng Li, Gang Wang, Jing Jin, Fuguo Xing

“…To further explore its antifungal mechanism, this study elucidated the functions of key pathway-related genes through a transcriptomics analysis. A total of 1402 differentially expressed genes (DEGs) were identified, including 987 up-regulated and 415 down-regulated genes. …”
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Transcriptomics and metabolomics profiling of Paris polyphylla var. yunnanensis with different growth years by Xiaoye Zhang, Jia Chen, Ping Xu, Xuan Zhang, Shuiyi Yang, Jie Zhang, Xiheng Wan, Yingsi Gao, Guowei Zheng

“…In this study, we collected samples of P. polyphylla aged 3 to 8 years for metabolome and transcriptome sequencing analysis. The total saponin content was found to be significantly higher in 8-year-old P. polyphylla compared to younger plants. …”
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Single-cell and spatial transcriptomic insights into glioma cellular heterogeneity and metabolic adaptations by Yixin Fu, Yong Yi, Yongxiang Shao, Jingcheng Jiang, Qingshan Deng

“…This review integrates recent advancements in single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics to elucidate glioblastoma’s cellular heterogeneity and metabolic reprogramming. …”
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Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and mammalian lung. by Weiling Zheng, Zhengyuan Wang, John E Collins, Robert M Andrews, Derek Stemple, Zhiyuan Gong

“…Our comparative analyses also provide molecular evidence of the relatedness of the fish swimbladder and mammalian lung.…”
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Evaluation and Interpretation of Transcriptome Data Underlying Heterogeneous Chronic Obstructive Pulmonary Disease by Seokjin Ham, Yeon-Mok Oh, Tae-Young Roh

“…Our extensive evaluation of COPD transcriptome data could provide guidelines for analyzing heterogeneous gene expression profiles and classifying potential candidate genes that are responsible for the pathogenesis of COPD.…”
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Physiological and transcriptomic profiles of tobacco seedling leaves in response to high chloride accumulation by Yunjie Wu, Jialing Lu, Dongxu Wang, Yuanyuan Li, Zhiyu Feng, Xiefeng Ye

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Integrating single-cell and spatial transcriptomics reveals the cellular heterogeneity of vestibular schwannoma by Wenqi Dong, Yuchen Jin, Lingkang Dong, Yumeng Jiang, Zhuangzhuang Li, Maoxiang Xu, Jingjing Wang, Feng Liu, Dongzhen Yu

“…In this study, we analyzed single-cell RNA sequencing (scRNA-seq) data from three previously published vestibular schwannomas (VS1-3), along with spatial transcriptomics data from two additional specimens (VS_S1-2). …”
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De novo assembly of transcriptomes of six Hua species (Semisulcospiridae, Cerithioidea, Gastropoda) by Sheng Zeng, Yuanzheng Meng, Zeyang Lin, Deyuan Yang, Yanjie Zhang, Shengchang Yang

“…This study provides valuable transcriptomic resources for the six Hua species, which can be used for various research of Semisulcospiridae, including biodiversity, phylogeny, and comparative genomics.…”
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Comparative transcriptome analysis in two contrasting genotypes for Sclerotinia sclerotiorum resistance in sunflower. by Mingzhu Zhao, Bing Yi, Xiaohong Liu, Dexing Wang, Dianxiu Song, Enyu Sun, Liangji Cui, Jingang Liu, Liangshan Feng

“…Here, a comparative transcriptomic analysis was performed in leaves of two contrasting sunflower genotypes, disease susceptible (DS) B728 and disease resistant (DR) C6 after S. sclerotiorum inoculation. …”
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Unraveling developmental gene regulation in holometabolous insects through comparative transcriptomics and proteomics by Maya Wilkens, Susanne Zimbelmann, Franziska Roth, Jasmin Cartano, Sergi Sayols, Mario Dejung, Michal Levin, Falk Butter

“…Here, we provide a comprehensive paired transcriptome and proteome dataset of 17 timepoints across the developmental life cycle of the silkworm Bombyx mori. …”
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A spatio-temporal transcriptomic and proteomic dataset of developing Brassica napus seeds by Dominic Knoch, Nils Rugen, Johannes Thiel, Marc C. Heuermann, Markus Kuhlmann, Paride Rizzo, Rhonda C. Meyer, Steffen Wagner, Jos H. M. Schippers, Hans-Peter Braun, Thomas Altmann

“…Here, we investigated the dynamics of seed development by an integrative analysis of the seed transcriptome and proteome. Plants of the winter-type cultivar Express 617 were grown under controlled, field-like conditions in the IPK PhenoSphere, and developing seeds were collected for temporally and spatially resolved multi-omics analyses. …”
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Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes by Brian Cox, Thomas Kislinger, Dennis A Wigle, Anitha Kannan, Kevin Brown, Tadashi Okubo, Brigid Hogan, Igor Jurisica, Brendan Frey, Janet Rossant, Andrew Emili

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Transcriptome-wide identification of 5-methylcytosine by deaminase and reader protein-assisted sequencing by Jiale Zhou, Ding Zhao, Jinze Li, Deqiang Kong, Xiangrui Li, Renquan Zhang, Yuru Liang, Xun Gao, Yuqiang Qian, Di Wang, Jiahui Chen, Liangxue Lai, Yang Han, Zhanjun Li

“…This antibody-free and bisulfite-free approach provides transcriptome-wide editing regions which are highly overlapped with the publicly available bisulfite-sequencing (BS-seq) datasets and allows for a more stable and comprehensive identification of the m5C loci. …”
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Integrated transcriptomic and metabolomic analysis reveals drivers of protein and oil variation in cottonseed by Chaoze Zhou, Yiwen Huang, Dayu Zhou, Yuzhen Wu, Shouyang Fu, Longyu Huang, Jun Peng, Meng Kuang

“…This study explored the regulatory mechanisms behind these differences by analyzing protein and oil accumulation patterns, transcriptomics, and metabolomics in two cotton varieties during seed development. …”
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Dissecting small cell carcinoma of the esophagus ecosystem by single-cell transcriptomic analysis by Hao-Xiang Wu, Yu-Kun Chen, Ying-Nan Wang, Jia-Ying Chen, Shu-Jing Xiang, Ying Jin, Zi-Xian Wang, Chun-Yu Huang, Lu-Ping Yang, Ye He, Wen-Long Guan, Long Bai, Yan-Xing Chen, Min Wang, Chao-Ye Wang, Run-Jie Huang, Yue Huang, Jin-Ling Zhang, Zhi-Da Lv, Si-Qi Yang, Rui-Hua Xu, Qi Zhao, Feng Wang

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Bering: joint cell segmentation and annotation for spatial transcriptomics with transferred graph embeddings by Kang Jin, Zuobai Zhang, Ke Zhang, Francesca Viggiani, Claire Callahan, Jian Tang, Bruce J. Aronow, Jian Shu

“…Abstract Single-cell spatial transcriptomics can provide subcellular resolution for a deep understanding of molecular mechanisms. …”
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Transcriptomic Profiling Reveals Key Genes Underlying Cold Stress Responses in Camphora by Bowen Shi, Linlin Zheng, Yifeng Wang, Qirui Wang

“…This study seeks to elucidate the molecular basis of cold tolerance through comparative transcriptomic analysis complemented by physiological characterization. …”
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Whole blood transcriptomics analysis of Indonesians reveals translocated and pathogenic microbiota in blood. by Katalina Bobowik, Muhamad Fachrul, Chelzie Crenna Darusallam, Pradiptajati Kusuma, Herawati Sudoyo, Clarissa A Febinia, Safarina G Malik, Christine A Wells, Irene Gallego Romero

“…Unequal investment in medical funding throughout Indonesia, particularly in rural areas, has resulted in under-reporting of cases, making surveillance challenging. Here, we use transcriptome data from 117 healthy individuals living on the islands of Mentawai, Sumba, and the Indonesian side of New Guinea Island to explore which pathogens are present within whole blood. …”
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