qRT-PCR Reference Gene Selection for the Discoloration of Tender Leaves in Hawk Tea (<i>Litsea coreana</i>) by Qianli Dai, Min Lu, Ximeng Yang, Chenggong Lei, Feiyi Huang, Xueping Hu, Xin Huang, Xiaolong Nie, Daojing Chen, Sicheng Huang, Hengxing Zhu

“…To identify stable reference genes for qRT-PCR analysis across different developmental stages and color variations of tender leaves in <i>Litsea coreana</i>, seven candidate reference genes were selected based on existing transcriptome data. qRT-PCR was performed on tender leaves of <i>L. coreana</i> at various stages and under different color conditions. …”
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Microenvironment-adaptive nanomedicine MXene promotes flap survival by inhibiting ROS cascade and endothelial pyroptosis by Ningning Yang, Rongrong Hua, Yingying Lai, Peijun Zhu, Jian Ding, Xianhui Ma, Gaoxiang Yu, Yiheng Xia, Chao Liang, Weiyang Gao, Zhouguang Wang, Hongyu Zhang, Liangliang Yang, Kailiang Zhou, Lu Ge

“…Mechanistically, MXene facilitated in situ angiogenesis, mitigated oxidative stress, suppressed pro-inflammatory pyroptosis, and activated the PI3K-Akt pathway, particularly influencing vascular endothelial cells. Comparative transcriptome analysis of skin tissues with and without MXene treatment provided additional evidence, highlighting mechanisms such as pro-inflammatory pyroptosis, ROS metabolic processes, endothelial cell proliferation regulation, and PI3K-Akt signaling pathway activation. …”
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A dynamic molecular landscape in colorectal cancer progression at single-cell resolution by Jianwen Sheng, Nianshuang Li, Shuai Li, Yuman Ye, Yuanhang Liao, Yupeng Zhang, Huan Chen, Mengxian Tu, Guping Zhong, Chaoliang Xiong, Pan Zheng, Yuting Lei, Zekun He, Xingxing He, Yao Zhang, Lei Wang, Xiaolin Gao, Yin Zhu, Jianping Liu, Huizhen Fan

“…Conclusions Our extensive transcriptome dataset provides valuable insights and acts as a fundamental resource to deepen our understanding of the complex molecular landscape in CRC. …”
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Pan-Genome Identification and Expression Analysis of Lipoxygenase Genes in Cucumber by Haiyu Xu, Kun Liu, Lili Zhao, Chunhua Chen, Lina Wang, Zhonghai Ren

“…Notably, <i>CsLOX22</i> responded to heat, cold, DM, and GM stresses. Our results provided a reference for further exploring the functions of <i>CsLOXs</i> in cucumber.…”
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A Nextflow pipeline for T-cell receptor repertoire reconstruction and analysis from RNA sequencing data by Teresa Rubio, Maria Chernigovskaya, Susanna Marquez, Cristina Marti, Paula Izquierdo-Altarejos, Amparo Urios, Carmina Montoliu, Vicente Felipo, Ana Conesa, Victor Greiff, Sonia Tarazona

“…Moreover, a step-by-step pipeline for the processing of transcriptome RNA-seq reads to deliver immune repertoire data is missing, and these types of analyses are usually not included in RNA-seq studies of immunological conditions. …”
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Analysis of CYP701A1 genes in gossypium species and functional characterization through gene silencing by Zhao Liang, Di Jiachun, Guo Qi, Xu Zhenzhen, Zhao Jun, Xu Peng, Xu Jianwen, Liu Jianguang, Shen Xinlian, Chen Xusheng

“…Enrichment analysis through KEGG pathway highlighted ‘Plant hormone signal transduction’ as a prominent pathway with 234 differentially expressed genes. The study provided insights into the function and regulatory network of the gene.…”
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A chromosome-level Dendrobium moniliforme genome assembly reveals the regulatory mechanisms of flavonoid and carotenoid biosynthesis pathways by Jiapeng Yang, Qiqian Xue, Chao Li, Yingying Jin, Qingyun Xue, Wei Liu, Zhitao Niu, Xiaoyu Ding

“…By integrating the genome and transcriptome, we identified biosynthesis pathway enzyme genes related to flavonoids, polysaccharides, carotenoids, and alkaloids. …”
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Nano-zinc oxide (nZnO) targets the AMPK-ULK1 pathway to promote bone regeneration by Xiu Chen, Zhenkun Weng, Hongchao Zhang, Jian Jiao, Jingjia Liang, Jin Xu, Dongmei Wang, Qian Liu, Qing Yan, Aihua Gu

“…Methods This study aimed to identify the molecular mechanisms how nZnO promoted osteogenic differentiation and bone regeneration using transcriptome analysis, drug intervention, and shRNA knockdown techniques, etc. …”
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Production, Passaging Stability, and Histological Analysis of Madin–Darby Canine Kidney Cells Cultured in a Low-Serum Medium by Ming Cai, Yang Le, Zheng Gong, Tianbao Dong, Bo Liu, Minne Su, Xuedan Li, Feixia Peng, Qingda Li, Xuanxuan Nian, Hao Yu, Zheng Wu, Zhegang Zhang, Jiayou Zhang

“…The transcriptome analysis showed that differentially expressed genes were predominantly enriched in the metabolic pathway and MAPK signaling pathway, indicating an activated state. …”
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Physiological and molecular insights into the effect of a seaweed biostimulant on enhancing fruit yield and drought tolerance in tomato by Aakansha Kanojia, Rafe Lyall, Neerakkal Sujeeth, Saleh Alseekh, Félix J. Martínez-Rivas, Alisdair R. Fernie, Tsanko S. Gechev, Veselin Petrov

“…ANF-treated plants exhibited enhanced growth, fruit yield, and stress tolerance under both moderate and severe drought conditions compared to untreated plants. Transcriptomic studies in leaves revealed that the priming treatment preserved the photosynthetic machinery, inducing stress-protective genes involved in ascorbate, peroxidase, GABA, glutathione, and flavanol biosynthesis. …”
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FimC binds to the promoter region of agn43 to modulate autoaggregation by Zhihao Wang, Xiangpeng Niu, Ningyuan Zhong, Lanfang Kong, Saqib Nawaz, Haiyang Zhang, Wei Jiang, Yuanyuan Liu, Jian Tu, Xiangan Han

“…It also highlights the importance of fimC in the biofilm formation and adhesion ability of APEC, which provides new insights into the functions of the fimbrial chaperone protein FimC.…”
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An ovarian insulin-like peptide specifically regulates energy allocation and oocyte development in nutrition-restricted cockroaches by Yuan Luo, Wen-Xin Hou, Shan-Shan Zhao, Yun-Long Cheng, Ke-Jia Zhang, Liang-Guan Lin, Sheng Li, Xiao-Jin Pei

“…Results In this study, we demonstrate that the ovary plays a crucial role in promoting vitellogenin biosynthesis and oocyte development under nutrition-restricted conditions through hemiovariectomy. Employing transcriptome analysis, RNAi screening, and fluorescence in situ hybridization, we identified an ovarian-enriched insulin-like peptide gene (BgILP2) that is dramatically upregulated during low nutrition conditions. …”
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GWAS and RNA-seq reveal novel loci and genes of low-nitrogen tolerance in cucumber (Cucumis sativus L.) by Huaxiang Wu, Huiming Yan, Bowen Li, Yike Han, Yike Han, Nan Liu, Mengyu Fan, Yahan Liu, Mingjie Lyu, Shengli Du, Shengli Du, Shengli Du, Aimin Wei, Aimin Wei

“…Collectively, this study provides novel genetic resources for improving NUE in cucumber breeding programs.…”
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New insights into developmental biology of Eimeria tenella revealed by comparative analysis of mRNA N6-methyladenosine modification between unsporulated oocysts and sporulated oocy... by Qing Liu, Bingjin Mu, Yijing Meng, Linmei Yu, Zirui Wang, Tao Jia, Wenbin Zheng, Wenwei Gao, Shichen Xie, Xingquan Zhu

“…In the present study, we surveyed the transcriptome-wide prevalence of m6A in sporulated oocysts and unsporulated oocysts of E. tenella. …”
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The intratumoral microbiota heterogenicity is related to the prognosis and tumorigenesis of cervical cancer by Yi Guo, Yuhang Xiao, Changyi Zhang, Ying Wang, Guangxu Cao, Ka Yu Tse, Zhiqiang Han, Zhiqiang Han, Fang Li, Yong Zhi

“…The clinical characteristics of patients with relatively high abundance of Pseudomonas had the higher levels of fibrinogen and lower levels of white blood cell (WBC) and albumin (ALB) expression. Combining transcriptome data from the two our collective CC and TCGA-CESC cohorts, we found that Pseudomonas abundance was significantly associated with fibrinogen beta peptide expression and worse overall survival in CC patients. …”
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Comparative response mechanisms of two cultivars of Musa paradisiaca L. to Fusarium oxysporum f.sp. cubense infection by Yajie Duan, Yajie Duan, Zhiwei Jia, Zhiwei Lu, Huigang Hu, Rulin Zhan

“…Through the perspective of transcriptome data, we focused on genes associated with lignin and cell wall development for Q-PCR validation. …”
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Comprehensive Genome-Wide Characterization of L-Type Lectin Receptor-like Kinase (L-LecRLK) Genes in Wheat (<i>Triticum aestivum</i> L.) and Their Response to Abiotic Stress by Wan Zhao, Fuyan Zhang, Jiahuan Wang, Shuai Fang, Zhongjie Cheng, Xuhui Ma, Jialin Fan, Zhaoshi Xu, Xiaojie Chen

“…Promoter analysis revealed a <i>cis</i>-element associated with hormone signaling and abiotic stress responses. Transcriptome profiling showed that <i>TaL-LecRLKs</i> exhibit tissue- and stage-specific expression patterns. …”
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Study on the Regulatory Mechanisms of Carapace Marking Formation in <i>Marsupenaeus japonicus</i> by Panpan Wang, Jiawei Zhu, Huanyu Chen, Qingyuan Hu, Zhenxiang Chen, Wenjia Li, Ting Yang, Jin Zhu, Binlun Yan, Huan Gao, Chaofan Xing

“…In a previous study, we used comparative transcriptome technology to screen some functional genes related to body color regulation. …”
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Genetically supported causal genes for rheumatoid arthritis: Mendelian randomization and co‐localization analyses by Yuanyuan Niu, Fan Su, Simin Chen, Jingnan Wang, Shuoyang Zhang, Ruiru Li, Yu Kuang, Liuqin Liang, Youjun Xiao, Hanshi Xu

“…Methods We used two transcriptome datasets to identify expression quantitative trait loci as the exposure and employed genome‐wide association studies data from the FinnGen study as the outcome. …”
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Analysis of Alternative Splicing Events and Identification of Key Genes in <i>Brassica napus</i> Leaves Infected by <i>Leptosphaeria biglobosa</i> by Xinning Ma, Lin Yuan, Jiuru Huangfu, Mengjiao Yan, Chen Guo, Lili Zhao, Hongxia Sun, Xiaoqing Jia, Ziqin Li, Haiyan Huangfu

“…Here, we used the Illumina Novaseq sequencing platform to conduct transcriptome sequencing on canola (<i>Brassica napus</i>) leaves infected with the blackleg pathogen (<i>Leptosphaeria biglobosa</i> strain nm⁻¹) at 0 h, 72 h, 120 h, and 168 h post-inoculation to investigate the mechanism of AS coordination with transcriptional regulation in canola’s response to blackleg disease. …”
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