A dual platform approach to transcript discovery for the planarian Schmidtea mediterranea to establish RNAseq for stem cell and regeneration biology. by Martin J Blythe, Damian Kao, Sunir Malla, Joanna Rowsell, Ray Wilson, Deborah Evans, Jamie Jowett, Amy Hall, Virginie Lemay, Sabrina Lam, A Aziz Aboobaker

“…However, the establishment of massively parallel sequencing technologies has provided the opportunity to define genetic content, and in particular transcriptomes, in unprecedented detail. …”
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Exploring the longitudinal expression dynamics of midguts in adult female Amblyomma americanum ticks by Stephen Lu, Lucas C. de Sousa-Paula, Jose M. C. Ribeiro, Lucas Tirloni

“…Despite this, our overall understanding of tick midgut biology is limited. Results Our transcriptome analysis identified 15,599 putative DNA coding sequences (CDS), which were classified into 26 functional groups. …”
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Enriching Genomic Resources and Marker Development from Transcript Sequences of Jatropha curcas for Microgravity Studies by Wenlan Tian, Dev Paudel, Wagner Vendrame, Jianping Wang

“…To enrich the jatropha genomic databases and resources for microgravity studies, we sequenced and annotated the transcriptome of jatropha and developed SSR and SNP markers from the transcriptome sequences. …”
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Multiomic Analysis of Environmental Effects and Nitrogen Use Efficiency of Two Potato Varieties Under High Nitrogen Conditions by Shuo Gao, Guowei Wei, Yuan Chang, Yanbin Yin, Qiaorong Wei, Ying Shi

“…The genes related to N efficiency were jointly identified using transcriptome and metabolome analyses. Significant difference was observed between the two varieties of microorganisms, leading to different rhizosphere microorganisms. …”
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The Cold Atmospheric Plasma Inhibits Cancer Proliferation Through Reducing Glutathione Synthesis by Qiyu Yang, Wei Zhao, Lingling Yang, Yongqin Fan, Changsheng Shao, Tao Wang, Fengqiu Zhang

“…Transcriptome data confirmed CAP’s role in oxidation-reduction reactions and glutamine metabolism. (4) Conclusions: This study provides the first mechanistic insights into CAP’s anticancer effects by targeting glutamine metabolism. …”
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Mutational Landscapes of Sequential Prostate Metastases and Matched Patient Derived Xenografts during Enzalutamide Therapy. by Manish Kohli, Liguo Wang, Fang Xie, Hugues Sicotte, Ping Yin, Scott M Dehm, Steven N Hart, Peter T Vedell, Poulami Barman, Rui Qin, Douglas W Mahoney, Rachel E Carlson, Jeanette E Eckel-Passow, Thomas D Atwell, Patrick W Eiken, Brendan P McMenomy, Eric D Wieben, Gautam Jha, Rafael E Jimenez, Richard Weinshilboum, Liewei Wang

“…Tissue biopsies from a metastatic rib lesion were obtained for sequencing before and after initiating enzalutamide treatment over a twelve-week period and also implanted subcutaneously as well as under the renal capsule in immuno-deficient mice. The genome and transcriptome landscapes of xenografts and the original patient tumor tissues were compared by performing whole exome and transcriptome sequencing of the metastatic tumor tissues and the xenografts at both time points. …”
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The immune system in cardiovascular diseases: from basic mechanisms to therapeutic implications by Xiaoyan Wang, Liming Chen, Jianming Wei, Hao Zheng, Ning Zhou, Xinjie Xu, Xin Deng, Tao Liu, Yunzeng Zou

“…Remarkably, based on the progress in basic research on immune responses in the cardiovascular system, significant advancements have also been made in pre-clinical and clinical studies of immunotherapy. This review provides an overview of the role of immune system in the cardiovascular system, providing in-depth insights into the physiological and pathological regulation of immune responses in various CVDs, highlighting the impact of multi-level regulation of immune responses in CVDs. …”
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MCT4: a key player influencing gastric cancer metastasis and participating in the regulation of the metastatic immune microenvironment by Tao Jiang, Jingcheng Zhang, Sicheng Zhao, Mingsi Zhang, Yunhai Wei, Xiaojuan Liu, Shuo Zhang, Wei Fan, Yueying Liu, Yuanlin Lv, Guangji Zhang

“…Methods In this study, we comprehensively utilized single-cell sequencing and external transcriptome sequencing databases to deeply analyze the mechanism of the impact of MCT4 on gastric cancer and its microenvironment. …”
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Automation of RNA-Seq Sample Preparation and Miniaturized Parallel Bioreactors Enable High-Throughput Differential Gene Expression Studies by Karlis Blums, Josha Herzog, Jonathan Costa, Lara Quirico, Jonas Turber, Dirk Weuster-Botz

“…The expected differences in cellular responses identified in this study show a promising approach for transcriptomic profiling of bioreactor cultures, providing valuable insights on a molecular level at-line in a high-throughput fashion.…”
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Multi-Omics Unveils Inflammatory Regulation of Fermented Sini Decoction Dregs in Broilers Infected with Avian Pathogenic <i>Escherichia coli</i> by Shuanghao Mo, Xin Fang, Wenxi Xiao, Bowen Huang, Chunsheng Li, Hui Yang, Yilin Wu, Yiming Wang, Hongxia Ma

“…These findings demonstrate that fermented liquid of Sini decoction dregs offers a promising, sustainable approach to control avian colibacillosis, mitigate antibiotic resistance, and improve poultry health, providing a scientific foundation for its application in farming to reduce economic losses and enhance food safety.…”
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A Fragment Insertion of <i>AgDFR</i> Results in a White Flower Phenotype in <i>Arundina graminifolia</i> (Orchidaceae) by Jie Li, Yonglu Wei, Jianpeng Jin, Jie Gao, Qi Xie, Fengxi Yang, Genfa Zhu

“…The developed molecular marker enables reliable differentiation of white-flowered variants from pigmented counterparts, providing valuable tools for germplasm management and breeding programs.…”
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TIPE regulates glucometabolic reprogramming by modulating LDHA expression in triple-negative breast cancer by HU Wei, REN Xiaomeng, WANG Yang, ZHAO Peiqing, CAO Kai

“…Methods: Stable TIPE-knockdown MDA-MB-231 cell lines were established using a lentiviral shRNA system and selected with puromycin. Transcriptome sequencing was used to analyze TIPE's impact on TNBC glycolytic pathways. …”
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Flavor compound geraniol induces inhibited nutrient utilization and developmental toxicity on embryonic–larval zebrafish by Yumin Luo, Run Han, Zhengyu Ren, Nana Ai, Shaowen Yu, Simon Ming‐Yuen Lee, Wei Ge, Ying Chen, Ying Zheng

“…This study establishes an efficient screening model for identifying toxic flavor compounds during developing stages, thereby elucidating the potential safety risks of geraniol exposure in zebrafish and providing a comprehensive understanding of its potential toxicity mechanism.…”
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Spatial host-microbiome profiling demonstrates bacterial-associated host transcriptional alterations in pediatric ileal Crohn’s disease by Sooyoung Jang, Eun Joo Lee, Sowon Park, Hyeji Lim, Byungsoo Ahn, Yoon Huh, Hong Koh, Yu Rang Park

“…Conclusions Our spatial host-microbiome profiling approach enables simultaneous species-level identification of bacteria and host transcriptomics. It reveals the intricate interactions between host cells and bacteria, providing cellular-level insights into CD pathogenesis. …”
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Single-cell RNA sequencing technology was employed to construct a risk prediction model for genes associated with pyroptosis and ferroptosis in lung adenocarcinoma by Longfei Ji, Binyu Wang, Danfei Shi, Weiyun Shen, Xinmin Li, Yong Li

“…Our findings reveal the interaction mechanism between pyroptosis, ferroptosis, and tumor immunity, providing new ideas and targets for precise treatment of LUAD.…”
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Mitochondrial functional impairment in ARL3‐mutation related rod‐cone dystrophy by Xiaoli Zhang, Shun Yao, Lujia Zhang, Beisi Zhang, Mingzhu Yang, Qingge Guo, Jin Xu, Zhongfeng Wang, Bo Lei, Xiuxiu Jin

“…Our study demonstrated that ARL3‐related mutations play a significant role in the diversity of mitochondrial function, providing novel insights into the functional analysis of ARL3‐related mutations.…”
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Exploring the tumor microenvironment of breast cancer to develop a prognostic model and predict immunotherapy responses by Ye Tian, Yong Yang, Lei He, Xiaocheng Yu, Hu Zhou, Juan Wang

“…The prognostic model accurately discriminated between patients classified as high- and low-risk, providing precise prognostic predictions for individual patients. …”
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Unveiling Ventilator-Associated Pneumonia: S100A8 as a Promising Biomarker Through Integrated RNA-Seq Analysis by Wang Q, Dong J, Jing X, Long Y, Jia H, Li Y, Wang J

“…There was an urgent need for new diagnostic biomarkers for VAP.Methods: The transcriptome of VAP patients was analyzed and computed using bioinformatics techniques in this study. …”
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An Insight into Differentially Expressed Genes and MicroRNAs in the Pituitary Glands of the Two Estrous Phases of Sheep with Different <i>FecB</i> Genotypes by Yue Zhang, Xiaoyun He, Ran Di, Xiangyu Wang, Mingxing Chu

“…These findings elucidate the impact of pituitary miRNAs on follicular development influenced by <i>FecB</i> gene mutation, providing valuable insights into sheep breeding.…”
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Identification and functional characterization of JrbZIP40 in walnut reveals its role in salt and drought stress tolerance in transgenic Arabidopsis seedlings by Jinyu Wei, Chang Jiao, Xi-Yu Li, Xuemin Li, Xin-Yi Zhang, Yongxu Wang, Yang Song, Kaiyu Yang, Yushi Liu, Jingran Zhang, Mengyao Liu, Yi-Lin Liang, Xinyue Wang, Han Li, Peng Jia, Xuemei Zhang, Guohui Qi, Qinglong Dong

“…Conclusions Overall, this study elucidates the regulatory network and biological functions of JrbZIP40 in drought and salt tolerance, providing a theoretical foundation and candidate gene resources for the future use of genetic engineering to improve walnut stress resistance.…”
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