Integrative single-cell and spatial transcriptomics analysis reveals MDK-NCL pathway’s role in shaping the immunosuppressive environment of lung adenocarcinoma by Yu Fu, Song Li, Yikang Zhao, Xiran Zhang, Xiaolu Mao, Ran Xu

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Integrated Metabolome and Transcriptome Analysis Reveals the Key Bitter Substances of <i>Pleioblastus amarus</i> Shoots at Different Developmental Stages by Limei Gong, Weijin Shi, Chunyan Mou, Shixing Zhou, Lin Xiao, Hongling Hu, Lihua Tu, Guirong Hou, Wei Ding, Congde Huang, Gang Chen

“…BT2 comparisons, respectively. An integrated analysis of metabolomic and transcriptomic data indicated that the metabolites and genes associated with the biosynthesis pathways of phenylalanine, tyrosine, tryptophan, arginine, and the branched-chain amino acids valine, leucine, and isoleucine were significantly enriched during the growth of <i>P. amarus</i> shoots. …”
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A Comprehensive Transcriptomic and Proteomics Analysis of Candidate Secretory Proteins in Rose Grain Aphid, <i>Metopolophium dirhodum</i> (Walker) by Atsbha Gebreslasie Gebrekidan, Yong Zhang, Julian Chen

“…Meanwhile, the proteomic analysis result identified, 15 salivary proteins. Interestingly, most salivary proteins (i.e., 60% of the proteins) showed close similarity to <i>A. craccivora</i>, while 46.67% showed close similarity to <i>A. glycines</i>, <i>M. sacchari</i> and <i>S. flava</i>. …”
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UV-Induced Mutants of <i>Metarhizium anisopliae</i>: Improved Biological Parameters, Resistance to Stressful Factors, and Comparative Transcriptomic Analysis by Hao Gao, Yingjie Luo, Qiming Li, Jiaxuan Guo, Bin Wang

“…Among them, the mutant MaUV-22 exhibited enhanced tolerance to heat, oxidative, osmotic, and SDS stresses as well as increased virulence against <i>Galleria mellonella</i>. Moreover, the transcriptome analysis of MaUV-22 revealed that the expression of genes associated with the heat shock protein pathway, glutathione S-transferase, and thioredoxin reductase were increased dramatically, while the expression of genes related to the catalase and superoxide dismutase pathways was downregulated. …”
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Transcriptome Analysis Reveals the Molecular Mechanism Involved in Carotenoid Absorption and Metabolism in the Ridgetail White Prawn <i>Exopalaemon carinicauda</i> by Yumin Han, Yang Yu, Chengsong Zhang, Shihao Li, Jianbo Yuan, Fuhua Li

“…To clarify the molecular mechanism of astaxanthin utilization in <i>Exopalaemon carinicauda</i> (<i>E. carinicauda</i>), we conducted a comparative transcriptome analysis on the intestine, hepatopancreas, and muscle of <i>E. carinicauda</i>, fed with an astaxanthin diet and a normal diet. …”
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Transcriptome Analysis of Effect of Cordyceps militaris Aqueous Extract in Human Gastric Cancer Cell BGC-823 on Different RCD Pathways by Mingqi CUI, Kaiwen YU, Yang SONG, Fangxu XU, Shenghou WANG, Ze WANG

“…A total of 5885 differentially expressed genes were identified through transcriptome sequencing analysis, with significant enrichment in the apoptosis (P=0.001) and autophagy (P=0.008) signaling pathways. …”
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Physiological and transcriptomic-based analysis reveal the common and specific pathways of clove basil (Ocimum gratissimum) organs in response to cadmium stress by Bin Wang, Yanhui Xiao, Xiao Yuan, Yukun Wang, Dengyue Jiang, Zhaoxia Zhan, Jinming He

“…RNA-Seq data was validated through qRT-PCR analysis, which confirmed the reliability of the transcriptomic results. …”
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Molecular mechanisms of flowering time differentiation revealed by transcriptomic sequencing and de novo analysis in Chinese invasive populations of Ambrosia artemisiifolia by Xiao-Feng Yang, Xiao-Meng Li, Pär K. Ingvarsson, Chao Xi, Wan-Jin Liao

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Molecular signatures diversity unveiled through a comparative transcriptome analysis of longissimus dorsi and psoas major muscles in Hanwoo cattle by Sunirmal Sheet, Sun Sik Jang, Jin-A. Lim, Woncheoul Park, Dahye Kim

“…Functional enrichment analysis revealed a tissue-specific response, as PM muscle showed increased lipid metabolism allied pathways, including the PPAR signaling pathway and regulation of lipolysis in adipocytes, while LD was characterized by growth and proliferative processes. …”
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Phylogenetic and transcriptomic analysis of chemosensory receptors in a pair of divergent ant species reveals sex-specific signatures of odor coding. by Xiaofan Zhou, Jesse D Slone, Antonis Rokas, Shelley L Berger, Jürgen Liebig, Anandasankar Ray, Danny Reinberg, Laurence J Zwiebel

“…Our phylogenetic analyses further demonstrate remarkably rapid gains and losses of ant Ors, while Grs and Irs have also experienced birth-and-death evolution to different degrees. …”
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RNA-Seq Transcriptomics and iTRAQ Proteomics Analysis Reveal the Dwarfing Mechanism of Blue Fescue (<i>Festuca glauca</i>) by Yong Zhang, Peng Han, Ruijie Zhao, Shuhan Yu, Hang Liu, Hong Wu, Jinyang Weng, Hengfeng Zhang

“…In this study, we investigated the dwarfing mechanism of <i>dw-1</i>, a blue fescue dwarfing mutant, using physiological, transcriptomic, and proteomic methods. The peroxidase (POD) enzyme activity and chlorophyll content of <i>dw-1</i> significantly increased, while the lignin, gibberellin (GA), and indoleacetic acid (IAA) content significantly decreased. …”
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Comparative transcriptome analysis and candidate gene mining for fire blight of Pear resistance in Korla fragrant Pear (Pyrus sinkiangensis Yü) by Yue Li, Yuanrong Ye, Wei Huan, Juan Ji, Jieyun Ma, Qiang Sheng, Jianfeng Lei

“…To this end, a comparative transcriptome analysis of common Korla fragrant pear (KFP, susceptible) and a bud mutation line (1910, resistant) at three inoculation periods was conducted. …”
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Genome Sequencing and Comparative Transcriptomic Analysis of Rice Brown Spot Pathogen <i>Bipolaris oryzae</i> Adaptation to Osmotic Stress by Chun Wang, Kexin Yang, Sauban Musa Jibril, Ruoping Wang, Chengyun Li, Yi Wang

“…Under 1.2 M sorbitol-induced osmotic stress, we observed significant differences in growth responses between RBD1 and the rice blast fungus <i>Magnaporthe oryzae</i> H7. Transcriptomic analysis using Illumina sequencing revealed that RBD1 responds to osmotic stress by enhancing carbohydrate metabolism, fatty acid degradation, and amino acid synthesis, while H7 primarily relies on protein synthesis to enhance growth tolerance. …”
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Integrative Analysis of Whole-Genome and Transcriptomic Data Reveals Novel Variants in Differentially Expressed Long Noncoding RNAs Associated with Asthenozoospermia by Maria-Anna Kyrgiafini, Maria Katsigianni, Themistoklis Giannoulis, Theologia Sarafidou, Alexia Chatziparasidou, Zissis Mamuris

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Integrated m6A RNA methylation and transcriptomic analysis of Apostichopus japonicus under combined high-temperature and hypoxia stress by Qiang Wang, Shuqing Zhang, Xiaohua He, Siyi Li, Xiaohui Xu, Yanwei Feng, Jianmin Yang, Guohua Sun

“…Results This study integrates m6A methylation sequencing (MeRIP-seq) and transcriptomic analysis (RNA-seq) to investigate molecular responses in A. japonicus under combined high-temperature (32 °C) and hypoxia (DO = 2 mg/L). …”
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Identification of long noncoding RNAs (lncRNAs) and co-transcriptional analysis of mRNAs and lncRNAs in transcriptomes of Anopheles gambiae by Jiannong Xu, Kai Hu, Michelle M. Riehle, Vedbar S. Khadka

“…IntroductionAnopheles gambiae is a primary malaria vector mosquito in Africa. RNA-seq based transcriptome analysis has been widely used to study gene expression underlying mosquito life traits such as development, reproduction, immunity, metabolism, and behavior. …”
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Liver Transcriptome Analysis Reveals a Potential Mechanism of Heat Stress Increasing Susceptibility to <i>Salmonella</i> Typhimurium in Chickens by Qi Zhang, Yvqing Zhu, Zixuan Wang, Qinghe Li, Guiping Zhao, Qiao Wang

“…Combined differential expression analysis and WGCNA identified three hub regulatory genes: <i>PTGDS</i> and <i>WISP2</i> showed significant correlations with the heterophil/lymphocyte ratio, while <i>SLC6A9</i> was significantly correlated with serum IL-8 levels. …”
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Comparative transcriptome analysis provides a glance into the regulation of the Krüppel homolog 1 on the reproduction and diapause of the predatory ladybeetle, Coccinella septempun... by Junjie Chen, Xiaoxiao Liu, Shunda Han, Maosen Zhang, Zhaohan Liu, Yuyan Li, Lisheng Zhang

“…DEGs analysis revealed significant transcriptional alterations between the Kr-h1 knockdown group and the control group. …”
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Microscopical Observation and Transcriptome Analysis Reveal the Effects of High‐Altitude Ecosystem in the Qualities of Different Genetic Varieties Brassica napus Resources by Zongji Zhang, Xionghua Li, Ri Ming, Yingying Lu, Qinwen Lin, Yafei Yang, Jialin Liao, Yunjuan Li, Lingli Mao, Yang Huang, Li Zhong, Yu Liang

“…Furthermore, histology microscopical observation showed cell size increased and cell density decreased in the shoot apical meristem (SAM) after bolting and at high altitude, compared to those cells before bolting and at low altitude. Transcriptome analysis showed that sucrose phosphate synthase (SPS), sucrose synthase (SUS), fructose‐1,6‐bisphosphate aldolase (FBA1), and alpha‐galactosidase (AGAL2) genes were significantly up‐regulated during the after‐bolting period at different altitude. …”
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Integrated metabolomic, transcriptomic and network analysis elucidates therapeutic mechanisms of Ganoderma lucidum spore oil against granulomatous pulmonary nodules by Ya Liu, Wendong Xu, Kexin Wang, Kexin Wang, Zhiye You, Xiaohong Chen, Xiaohong Chen, Huihui Ti, Xiaoli Liang, Lin Cao, Hongfei Cai, Juyan Liu, Zifeng Yang, Zifeng Yang, Zifeng Yang

“…Metabolomics, transcriptomics, and network analysis were employed to elucidate its mechanisms. …”
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