Transcriptomic and Metabolomic Exploration of the Therapeutic Effects of Prunus cerasifera Ehrh. Polyphenol on Metabolic-associated Fatty Liver Disease by Zaifu ZHOU, Yuxia WANG, Daohong CHEN, Hongbo REN, Quansong LIN

“…In summary, PCP has a significant therapeutic effect on MAFLD through the regulation of the transcriptome and bile acid metabolism, providing a scientific basis for its potential as a natural product for the treatment of MAFLD.…”
Get full text

Transcriptomics of HERVs reveals clinico-biological characterization of LTR5_Hs and HERVS71 loci in gastric cancer by Juan Xu, Jie Liu, Yanhuan Wang, Linjie Peng, Wang Li, Likai Ji, Yang Yang, Benshuai You, Yan Huang, Shikun Fang, Ping Ni, Wen Zhang, Chenglin Zhou

Get full text

Unraveling key transposable elements in pathogen-induced bovine mastitis through comparative in vivo and in vitro transcriptomic analysis by Songyan An, Siyuan Mi, Siqian Chen, Yongjie Tang, Yue Xing, Yi Jing, Ying Yu

Get full text

Bioinformatic Analysis of Apoptosis-Related Genes in Preeclampsia Using Public Transcriptomic and Single-Cell RNA Sequencing Datasets by Liu L, Li X, Yang H, Xu F, Dong X

“…Their decrease in early PE and increase in late PE reflected the placenta’s adaptation to adverse pregnancy conditions.Conclusion: Four ARGs, CD44, MIF, PIK3R1, and TLR4, identified through comprehensive analyses, served as significant biomarkers for PE and offered insights into PE’s cellular mechanisms of PE, providing valuable references for further research. …”
Get full text

Whole-transcriptome sequencing reveals the effects of acupuncture on early embryos post-IVF-ET in poor ovarian response by Jianheng Hao, Yuemeng Zhao, Xuan Liu, Huichao Xu, Liying Liu, Haijun Wang, Ying Lan, Laixi Ji

“…Therefore, this study aimed to investigate the molecular mechanisms by which acupuncture influences early embryo development in POR mice after IVF-ET through whole-transcriptome sequencing. Methods We established POR mice model and performed acupuncture treatment. …”
Get full text

Root Transcriptome Analysis Identifies Salt-Tolerance Genes in Sweet Corn Chromosome Segment Substitution Lines (CSSLs) by Zili Zhang, Xuxuan Duan, Pengfei Liu, Qingchun Chen, Wei Sun, Xiaorong Wan, Yixiong Zheng, Jianting Lin, Feng Jiang, Faqiang Feng

“…A hypothetical model, which established a multi-layered salt adaptation strategy, by integrating ROS detoxification, osmotic balance, and phytohormone signaling, was put forward. By integrating transcriptome and differential chromosomal fragment data, our findings identify 14 candidate genes for salt tolerance, providing potential ideal target genes in breeding to improve salt tolerance in sweet corn.…”
Get full text

A study on the hepatic response to heat stress in Gymnocypris eckloni through an approach combining metabolomic and transcriptomic profiling by Chaowei Zhou, Yuting Duan, Junting Li, Suxing Fu, Shuhao Bai, Yutong Zhuang, Shidong Liu, Hejiao Li, Yinhua Zhou, Qiming Wang, Jian Shen, Rongzhu Zhou, Luo Lei, Haiping Liu

“…Notably, integrated transcriptomic and metabolomic analysis suggested that tryptophan metabolism played an important role in the adaptation of G. eckloni to chronic heat stress. …”
Get full text

Integrative Transcriptome and Metabolome Analysis Identifies Potential Pathways Associated with Cadmium Tolerance in Two Maize Inbred Lines by Pingxi Wang, Min Li, Xingye Ma, Bin Zhao, Xining Jin, Huaisheng Zhang, Shilin Chen, Xiangyuan Wu, Xiaoxiang Zhang

“…The integrative analysis highlighted the crucial roles of phenylpropanoid biosynthesis and zeatin biosynthesis in C7_2 for resistance to Cd stress. This study provides novel insights into the molecular and metabolic pathways underlying Cd tolerance in maize by integrating transcriptomic and metabolomic analyses of two contrasting inbred lines, providing a theoretical foundation for the future breeding of Cd-tolerant varieties.…”
Get full text

A single-cell transcriptomic atlas of immune cells in Wilson disease identifies copper-specific immune regulation by Shuya Wang, Xianlei Sun, Qingxuan Xin, Jianxiang Shi, Jin Li, Huilin Zhang, Mengjiao Xue, Fanxiang Yin, Zan Qiu, Xiaoqian Wang, Nannan Sun, Yingmei Li, Yaoyao Chen, Liyan Fu, Chaoqi Li, Shaohua Yan, Xian Zhao, Bolin Jue, Yanxia Gao, Baohong Yue, Bo Qin, Yong Jiang, Rongqun Guo

“…Differential expression analysis was performed to identify WD-specific signatures by comparing transcriptome profiles of patients with WD with HDs. …”
Get full text

Integration of single-nuclei and spatial transcriptomics to decipher tumor phenotype predictive of relapse-free survival in Wilms tumor by Ran Yang, Ran Yang, Lulu Xie, Rui Wang, Yi Li, Yifei Lu, Baihui Liu, Shuyang Dai, Shan Zheng, Shan Zheng, Kuiran Dong, Kuiran Dong, Rui Dong, Rui Dong

“…Targeting these cells with EGFR inhibitors, in combination with conventional chemotherapy, may provide a potential therapeutic strategy for WT patients.…”
Get full text

Single cell and spatial transcriptomics highlight the interaction of club-like cells with immunosuppressive myeloid cells in prostate cancer by Antti Kiviaho, Sini K. Eerola, Heini M. L. Kallio, Maria K. Andersen, Miina Hoikka, Aliisa M. Tiihonen, Iida Salonen, Xander Spotbeen, Alexander Giesen, Charles T. A. Parker, Sinja Taavitsainen, Olli Hantula, Mikael Marttinen, Ismaïl Hermelo, Mazlina Ismail, Elise Midtbust, Maximilian Wess, Wout Devlies, Abhibhav Sharma, Sebastian Krossa, Tomi Häkkinen, Ebrahim Afyounian, Katy Vandereyken, Sam Kint, Juha Kesseli, Teemu Tolonen, Teuvo L. J. Tammela, Trond Viset, Øystein Størkersen, Guro F. Giskeødegård, Morten B. Rye, Teemu Murtola, Andrew Erickson, Leena Latonen, G. Steven Bova, Ian G. Mills, Steven Joniau, Johannes V. Swinnen, Thierry Voet, Tuomas Mirtti, Gerhardt Attard, Frank Claessens, Tapio Visakorpi, Kirsi J. Rautajoki, May-Britt Tessem, Alfonso Urbanucci, Matti Nykter

“…Here we present a comprehensive transcriptomic landscape of the prostate TME at multiple points in the standard treatment timeline employing single-cell RNA-sequencing and spatial transcriptomics data from 120 patients. …”
Get full text

Unraveling ScAPD1-mediated resistance mechanism to Verticillium dahliae through integrated host-pathogen transcriptomics by Qilin Yang, Ruirui Yang, Huan Zhang, Fangliu Yin, Leyi Wang, Daoyuan Zhang, Xiaoshuang Li

“…We employed an integrated host-pathogen transcriptomics approach (dual RNA-seq), alongside physiological and biochemical experiments. …”
Get full text

Comparative transcriptome analysis identifies genes associated with chlorophyll levels and reveals photosynthesis in green flesh of radish taproot. by Yuan-Yuan Li, Min Han, Rui-Hua Wang, Ming-Gang Gao

“…These findings suggested that photosynthesis occurred in the radish green flesh, which was also supported by the results of Chl fluorescence. Our study provides transcriptome data on radish taproots and provides new information on the formation and function of radish green flesh.…”
Get full text

Transcriptome analysis of the pectoral muscles of local chickens and commercial broilers using Ribo-Zero ribonucleic acid sequencing. by Yanhua Zhang, Donghua Li, Ruili Han, Yanbin Wang, Guoxi Li, Xiaojun Liu, Yadong Tian, Xiangtao Kang, Zhuanjian Li

“…The aim of this study was to provide a reference for studies of the differences in the meat quality and growth of different breeds of chickens.…”
Get full text

SpaCCC: Large Language Model-Based Cell-Cell Communication Inference for Spatially Resolved Transcriptomic Data by Boya Ji, Xiaoqi Wang, Debin Qiao, Liwen Xu, Shaoliang Peng

“…In summary, SpaCCC provides a sophisticated and practical tool allowing researchers to decipher spatially resolved cell-cell communications and related communication patterns and signaling pathways based on spatial transcriptome data. …”
Get full text

Single‐cell transcriptomics reveals distinct cell response between acute and chronic pulmonary infection of Pseudomonas aeruginosa by Xueli Hu, Mingbo Wu, Teng Ma, Yige Zhang, Chaoyu Zou, Ruihuan Wang, Yongxin Zhang, Yuan Ren, Qianqian Li, Huan Liu, Heyue Li, Taolin Wang, Xiaolong Sun, Yang Yang, Miao Tang, Xuefeng Li, Jing Li, Xiang Gao, Taiwen Li, Xikun Zhou

“…The dissection of immune system may provide a basis for effective therapeutic strategies against bacterial infection. …”
Get full text

Transcriptomic and Metabolomic Characterization of Volatile Flavor Compound Dynamics in Dragon Fruit (<i>Selenicereus</i> spp.) Development by Zhi-Jiang Wu, Ri-Wen Ji, Ze-Jian Huang, Xiao-Ying Ye, Li-Fang Huang, Hai-Yan Deng, Gui-Feng Lu, Shuo-Tong Wei, Chao-An Liu, Zhen-Ying Li, Hong-Li Li, Gui-Dong Liang

“…In conclusion, our results provide a theoretical basis for an in-depth understanding of the volatile flavor compounds in dragon fruit and provide new genetic resources for the subsequent study of fruit flavor compounds.…”
Get full text

Genomic and Transcriptomic Analysis of Mutant <i>Bacillus subtilis</i> with Enhanced Nattokinase Production via ARTP Mutagenesis by Liuyu Guo, Yang Chen, Zhiyong He, Zhaojun Wang, Qiuming Chen, Jie Chen, Fatih Oz, Zhimin Xu, Maomao Zeng

Get full text

Protocol for isolating and characterizing human vitreous immune cell infiltrates by flow cytometry and single-cell transcriptomic studies by Sandhya Rani Bhanja, Sayantan Ghosh, Pankaj Kumar, Tulasi Nagabandi, Arun Raina, Kaiser Alam, John V. Forrester, Soumyava Basu

“…Summary: Vitreous infiltrating immune cells represent an accessible tissue sample that can provide valuable information on the intraocular immune response without compromising the structural and functional integrity of the eye. …”
Get full text

Development and validation of machine learning-based diagnostic models using blood transcriptomics for early childhood diabetes prediction by Xin Huang, Xin Huang, Di Ouyang, Weiming Xie, Huawei Zhuang, Siyu Gao, Pan Liu, Lizhong Guo

“…Peripheral blood transcriptomic analysis provides a minimally invasive approach for identifying predictive biomarkers prior to clinical manifestation. …”
Get full text