A pluripotent stem cell atlas of multilineage differentiation by Sophie Shen, Tessa Werner, Han Sheng Chiu, Xiaoli Chen, Quan Nguyen, Nathan J. Palpant

“…Genome-wide and single-cell transcriptomics technologies likewise offer high-throughput analysis of heterogeneous cell differentiation states. …”
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Engineered reduction of S-adenosylmethionine alters lignin in sorghum by Yang Tian, Yu Gao, Halbay Turumtay, Emine Akyuz Turumtay, Yen Ning Chai, Hemant Choudhary, Joon-Hyun Park, Chuan-Yin Wu, Christopher M. De Ben, Jutta Dalton, Katherine B. Louie, Thomas Harwood, Dylan Chin, Khanh M. Vuu, Benjamin P. Bowen, Patrick M. Shih, Edward E. K. Baidoo, Trent R. Northen, Blake A. Simmons, Robert Hutmacher, Jackie Atim, Daniel H. Putnam, Corinne D. Scown, Jenny C. Mortimer, Henrik V. Scheller, Aymerick Eudes

“…Abstract Background Lignin is an aromatic polymer deposited in secondary cell walls of higher plants to provide strength, rigidity, and hydrophobicity to vascular tissues. …”
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Gibberellin-Induced Transcription Factor <i>Sm</i>MYB71 Negatively Regulates Salvianolic Acid Biosynthesis in <i>Salvia miltiorrhiza</i> by Cuicui Han, Xingwen Dong, Xiaowen Xing, Yun Wang, Xiaobing Feng, Wenjuan Sang, Yifei Feng, Luyao Yu, Mengxuan Chen, Hongyuan Hao, Taohong Huang, Bailin Li, Wenhui Wu, Zheng Zhou, Ying He

“…Here, we identified a GA-induced R2R3MYB transcription factor (TF), <i>Sm</i>MYB71, from a transcriptome library of GA-treated <i>S. miltiorrhiza</i>. …”
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Dual Roles of SIRT7 Inhibition by Oroxylin A Reprogram HSCs Fate: PRMT5 Succinylation-Driven Senescence and Ecto-Calreticulin-Dependent NK Cell Immune Clearance in Liver Fibrosis by Junrui Wang, Haoyuan Tian, Yuanyuan Gao, Xinran Qiu, Zhengyang Bao, Danli Zhao, Feng Zhang, Zili Zhang, Feixia Wang, Shizhong Zheng, Haibo Cheng, Jiangjuan Shao

“…This work establishes SIRT7 as a pivotal therapeutic target and provides mechanistic insights for developing antifibrotic strategies.…”
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snRNA-seq reveals subcutaneous white adipose tissue remodeling upon return to thermoneutrality after cold stimulation by Yusha Yang, Yusha Yang, Guanyu Zhang, Ting Yi, Ting Yi, Shuran Yang, Shuran Yang, Shuai Wu, Yongqiang Zhang, Li Zhang, Xi Li, Xiuxuan Wu, Xiuxuan Wu, Jun Li, Danfeng Yang

“…Subsequently, we employed single-nucleus RNA sequencing (snRNA-seq) to comprehensively characterize iWAT cellular dynamics during cold stimulation and the subsequent two-week period after the return to thermoneutrality.ResultsOur findings revealed that while iWAT phenotypically reverts to a white state after 2 weeks of rewarming, as evidenced by structural, functional, and bulk transcriptomic characteristics, significant cold-induced molecular and cellular signatures persist. …”
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RNF20/RNF40 supports the aggressive behavior in cervical cancer by regulating a peroxisome-based anti-ferroptotic mechanism by Shaishavi Jansari, Anna Blandau, Evangelos Prokakis, Daniela Grimm, Anja Maria Naßl, Stefan Küffer, Wiebke Möbius, Christian Dullin, Fernanda Ramos-Gomes, Leona Schüürhuis, Lena Fritsche, Laura Schridde, Matthias Plessner, Carolin. A. Bast, Fabian A. Gayer, Sven Thoms, Julia Gallwas, Florian Wegwitz

“…Conclusion Together, our results indicate that interfering with RNF20 and RNF40 driven H2Bub1 and the peroxisome transcriptional program could provide a novel target for a therapeutic approach against aggressive cervical cancer.…”
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Chromosome-level genome assembly of the synanthropic fly Chrysomya megacephala: insights into oviposition location by Lipin Ren, Ngando Fernand Jocelin, Fengqin Yang, Xiangyan Zhang, Yanjie Shang, Yakai Feng, Shan Chen, Wei Zhan, Xiaohong Yang, Wei Li, Jiasheng Song, Haojie Tang, Yequan Wang, Yong Wang, Changquan Zhang, Yadong Guo

“…This study not only provides valuable insights into the molecular mechanisms of oviposition localization in C. megacephala but also facilitates further research into the genetic diversity and phylogeny of the Calliphoridae family.…”
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Insights into the role of MSLN-positive circulating tumor cell as an auxiliary diagnostic biomarker in epithelial ovarian cancer by Hang Xu, Min Wang, Shuting Wu, Qinke Li, Jinlong Wang, Siying Zhang, Qiongming Liu, Mengting Wang, Ruifang Li, Zhiyuan Hu, Zhiyuan Hu, Yi Liu, Zhu Yang

“…The combination of MSLN(+)CTCs with CA125 provides an optimal balance between sensitivity and specificity, offering promising clinical utility for EOC diagnosis.…”
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Human urine stem cells protect against cyclophosphamide-induced premature ovarian failure by inhibiting SLC1A4-mediated outflux of intracellular serine in ovarian granulosa cells by Hao-Cheng Gu, Ling-Fang Wang, Yu-Wei Zhang, You-Qiong Zhuo, Zhou-Hang Zhang, Xing-Yu Wei, Quan-Wen Liu, Ke-Yu Deng, Hong-Bo Xin

“…The target genes of miRNA were accessed by transcriptome sequencing in GCs, and the underlying mechanisms were further elucidated. …”
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Immunoregulatory programs in anti‐N‐methyl‐D‐aspartate receptor encephalitis identified by single‐cell multi‐omics analysis by Xinhui Li, Yicong Xu, Weixing Zhang, Zihao Chen, Dongjie Peng, Wenxu Ren, Zhongjie Tang, Huilu Li, Jin Xu, Yaqing Shu

“…Methods Peripheral blood mononuclear cells (PBMCs) from patients in the acute phase of anti‐NMDARE and healthy controls were sequenced using single‐cell joint profiling of transcriptome and chromatin accessibility. Differential gene expression analysis, transcription factor activity profiling, and cell‐cell communication modeling were performed to elucidate the immune mechanisms underlying the disease. …”
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QTL mapping associated with Verticillium wilt resistance in cotton based on MAGIC population by Muhammad Ayyaz, Zewei Chang, Shugen Ding, Peng Han, Lin Xu, Abudurezike Abudukeyoumu, Irfan Ali Siddho, Zhibo Li, Hairong Lin, Jianwei Xu, Yuanlong Wu, Xinhui Nie

“…The screening of candidate genes was performed on the transcriptome derived from resistant and susceptible cultivars, combined with gene annotation and tissue expression patterns, and two key candidate genes, Ghir_A01G006660 and Ghir_A02G008980, were found to be potentially associated with Verticillium wilt resistance. …”
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Rumen microbiota regulates IMF deposition in Xizang sheep by activating the PPARγ transcription factor: a rumen-muscle axis perspective by Cheng Pan, Junru Pan, Yangzong Zhaxi, Haiyan Li, Zhenzhen Zhang, Feng Guan, Jiacuo Jinmei, Zhaxi Baijiu, Sangzhu Baima, Quzhu Yixi, Tianzeng Song, Wangsheng Zhao

“…This finding suggests that modulating the composition of the microbial community could serve as a strategy to improve the flavor of ruminant-derived food products. These insights provide valuable understanding of the complex interactions between rumen bacteria and mutton flavor, offering new approaches for research in this field.…”
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Enhancing infectious intestinal disease diagnosis through metagenomic and metatranscriptomic sequencing of 1000 human diarrhoeal samples by Edward Cunningham-Oakes, Blanca M. Perez-Sepulveda, Yan Li, Jay C. D. Hinton, Charlotte A. Nelson, K. Marie McIntyre, Maya Wardeh, Sam Haldenby, Richard Gregory, Miren Iturriza-Gómara, Christiane Hertz-Fowler, Sarah J. O’Brien, Nigel A. Cunliffe, Alistair C. Darby, on behalf of the INTEGRATE consortium

“…A comprehensive transcriptomic profile of Salmonella enterica serovar Enteritidis was recovered from the stool of a patient with a laboratory-confirmed Salmonella infection. …”
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The Knob Domain of the Fiber-1 Protein Affects the Replication of Fowl Adenovirus Serotype 4 by Xiaofeng Li, Zhixun Xie, You Wei, Zhiqin Xie, Aiqiong Wu, Sisi Luo, Liji Xie, Meng Li, Yanfang Zhang

“…These results demonstrate the role of the knob domain of the fiber-1 (fiber-1-Δ2) protein in FAdV-4 infection and provide a theoretical basis for analyzing the function of the fiber-1 protein of FAdV-4.…”
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The m6A modification regulates the composition of myofiber types in chicken skeletal muscle by Yanju Shan, Yifan Liu, Ming Zhang, Lichuan Pang, Gaige Ji, Xiaojun Ju, Yunjie Tu, Jingting Shu

“…Our results contribute to a better understanding of epigenetic factors involved in forming chicken myofiber-type properties and provide new targets for further investigation into chicken's growth development and meat quality.…”
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Dehydrodiisoeugenol targets the PLK1-p53 axis to inhibit breast cancer cell cycle by Lin Li, Yifan Zheng, Yongxia Yang, Senlin Shi, Shangjie Liu, Keying Huang, Luonan Qiu, Rongxin Zhang, Wenbin Huang, Wenbin Huang, Yin Leng

“…WGCNA, network pharmacology, molecular docking, transcriptome sequencing analysis, immune infiltration analysis and single-cell sequencing were used to explore the mechanism of DHIE on breast cancer. …”
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Unveiling the Temporal Dynamics and Molecular Regulation Profiles of Neutrophil Extracellular Traps Following Spinal Cord Injury by Li J, Chang C, Li Y, Cui S, Bai J, Zhang C, Wang X, Li K, Jian F

“…This study aimed to explore the temporal dynamics and key regulatory genes of NET formation in SCI to identify therapeutic targets.Methods: We integrated two transcriptomic datasets from the GEO database to identify differentially expressed NETs-related genes (NRGs) in SCI. …”
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Comprehensive Analysis of Programmed Cell Death-Related Genes in Diagnosis and Synovitis During Osteoarthritis Development: Based on Bulk and Single-Cell RNA Sequencing Data by Zhou J, Jiao S, Huang J, Dai T, Xu Y, Xia D, Feng Z, Chen J, Li Z, Hu L, Meng Q

“…Diverse programmed cell death (PCD) pathways are closely linked to the pathogenesis of OA, but few studies have explored the relationship between PCD-related genes and synovitis.Methods: The transcriptome expression profiles of OA synovial samples were obtained from the Gene Expression Omnibus (GEO) database. …”
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Multiomics profiles of genome-wide alterations in H3K27ac in different lung lobes after acute graft-versus-host disease with MSCs treatment by Zixuan Lu, Yuming Zhou, Yuming Zhou, Chengyu Li, A. M. Abd El-Aty, A. M. Abd El-Aty, Chengxia Liu, Xiying Luan, Bin Wang, Guoyan Wang, Guoyan Wang

“…In this study, we described 55 paired transcriptomes and genome-wide H3K27ac in five lung lobes, with groups designated as follows: control, GVHD, human placenta-derived MSC (hPMSC)-treated, and PBS-treated groups. …”
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Molecular characterization and expression profiles of cytochrome P450 reductase gene in Sogatella furcifera (Hemiptera: Delphacidae) by YU Hang, LIU Su, ZHU Qingzi, ZHOU Wenwu, LIANG Qingmei, SHI Xiaoxiao, ZHU Zijie, ZHU Zengrong

“…Finally, after exposure of deltamethrin, buprofezin and imidacloprid at sublethal concentrations for 6,12 and 24 h, the relative expression levels of SfCPR in the third-instar nymphs were investigated.By searching the transcriptome data sets of S. furcifera, a cDNA fragment encoding putative CPR (named SfCPR) was identified. …”
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