Metabolome and transcriptome analyses reveal the mechanism underlying the differences in skin development between the two duck breeds during embryonic stage by Zhigang Hu, Yingjie Cai, Chang Cao, Hua He, Shun Guo, Na Li, Aiguo Xin, Xiaolin Liu

“…The significantly different metabolites (SDMs) were mainly organoheterocyclic compounds, lipids and lipid-like molecules, organic oxygen compounds, organic acids and derivatives, including L-tyrosine, N-arachidonyl maleimide, glycerophospho-N-palmitoyl ethanolamine, LPE 22:4, and PC(0:0/18:0). which were mainly enriched in glycerophospholipid metabolism, arachidonic acid metabolism, linoleic acid metabolism, alpha-linoleic acid metabolism, and melanogenesis in metabolome, suggesting that these pathways may play important roles in skin development of duck during embryonic stage. Besides, the analysis of integrated transcriptome and metabolome indicated that the pathways, including glycerophospholipid metabolism, arachidonic acid metabolism, linoleic acid metabolism, and alpha-linolenic acid metabolism, could contribute to regulating skin development in embryonic duck. …”
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Decoding Flavonoid Metabolism for Nutritional Enhancement: A Transcriptome–Metabolome Integration Study of Biosynthesis in Edible <i>Chrysanthemum indicum</i> L. by Chengxiang Wang, Yong Su, Min Wei, Qiaosheng Guo, Qingjun Zou, Tao Wang

“…This study compared flavonoid metabolism in white mutant (BHYJ) and yellow (HJ06) varieties through integrated metabolomic and transcriptomic analyses. Metabolomics identified 491 flavonoids, revealing distinct accumulation patterns: BHYJ accumulated dihydroflavones/chalcones (eriodictyol, hesperetin-8-<i>C</i>-glucoside-3′-<i>O</i>-glucoside, naringenin chalcone), while HJ06 showed higher flavones/flavonols (linarin, rhoiflolin, vitexin, rutin, nicotiflorin). …”
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Identification and validation of reference genes for qRT-PCR analyses under different experimental conditions in Dendrobium nobile by Kaijie Li, Xianfen Deng, Yao Wu, Jinling Li, Mingjin Huang, Chunli Luo, Hualei Wang, Hongchang Liu, Dandan Li

“…Identifying stable reference genes (RGs) in D. nobile under various experimental conditions is essential for accurate quantitative real-time polymerase chain reaction (qRT-PCR) analysis. In this study, eight genes were selected as the candidate RGs based on the transcriptome data from different tissues of D. nobile. …”
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Multi-Omics Investigation of Fatty Acid Content Variations in Common Carp (<i>Cyprinus carpio</i>) Muscle: Integrating Genome, Transcriptome, and Lipid Profiling Data by Kaikuo Wang, Qi Wang, Yingjie Chen, Yiming Cao, Ran Zhao, Shuangting Yu, Xiaoqing Sun, Yan Zhang, Jiongtang Li

“…For the total PUFA (TPUFA) content, transcriptome analysis of groups with the highest and lowest TPUFA content identified 715 differentially expressed genes (DEGs), including genes involved in oxidation and ubiquitination. …”
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Longitudinal profiling of host response and oropharyngeal respiratory microbiome reveals dynamic alterations during recovery from community-acquired pneumonia by Lizhe Hong, Lijun Suo, Kang Chang, Hongyun Cao, Jiahui Luan, Fuxin Zhang, Xiaofeng Yu, Xiaohui Zou, Bo Liu, Bin Cao

“…To address this gap, we longitudinally collected CAP patients’ peripheral blood for transcriptome and oropharyngeal swabs for microbiome analysis from admission to 4 months post infection. …”
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A Novel Research Paradigm for Sarcopenia of Limb Muscles: Lessons From the Perpetually Working Diaphragm's Anti‐Aging Mechanisms by Enhui Li, Rui Wang, Yanli Li, Xiang Zan, Shufen Wu, Yiru Yin, Xiaorong Yang, Litian Yin, Yu Zhang, Jianguo Li, Xin Zhao, Ce Zhang

“…Methods Treadmill and grip tests assessed limb muscle function, while a lung function system evaluated respiratory function in both adult (6‐month‐old) and old (22‐month‐old) mice. …”
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Dying occurs as a defined molecular progression in Drosophila rather than as nonspecific physiological collapse by Andrew W. Scott, Andrew P.K. Wodrich, Hitesh S. Chaouhan, Arvind K. Shukla, Kory Johnson, Philip G. McQueen, Edward Giniger

“…We apply pseudotime trajectory analysis to transcriptomic data from individual flies as they approach death. …”
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Integrated spatial omics of metabolic reprogramming and the tumor microenvironment in pancreatic cancer by Hao Wu, Qiyao Zhang, Zhen Cao, Hongtao Cao, Mengwei Wu, Mengdi Fu, Tingping Huang, Xianlin Han, Xiaoyan Chang, Ziwen Liu

“…Pseudotime trajectory analysis revealed metabolic shifts along the malignant progression, while single-cell Metabolism (scMetabolism) delineated metabolic differences between pathological regions, classifying them as hypermetabolic or hypometabolic. …”
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Multi-omics whole-genome characterization of the copy number landscape of metastatic pancreatic ductal adenocarcinoma by James T. Topham, Joanna M. Karasinska, Andrew Metcalfe, Hassan A. Ali, Steve E. Kalloger, Maya Kevorkova, Emma Titmuss, Gian Luca Negri, Sandra E. Spencer, Gun Ho Jang, Grainne M. O’Kane, Richard A. Moore, Andrew J. Mungall, Jonathan M. Loree, Faiyaz Notta, Julie M. Wilson, Oliver F. Bathe, Patricia A. Tang, Rachel Goodwin, Gregg B. Morin, Jennifer J. Knox, Steven Gallinger, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, Daniel J. Renouf, David F. Schaeffer

“…Summary: Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive disease with limited therapeutic options. While genome profiling has benefitted clinical decision-making in many cancer types, PDAC remains among the most lethal solid cancers and has relatively few clinically actionable molecular targets. …”
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Exploring the Efficacy and Potential Mechanisms of Topical <i>Periplaneta americana</i> (L.) Extract in Treating Androgenetic Alopecia in a Mouse Model: A Systems Pharmacology and... by Tangfei Guan, Xin Yang, Canhui Hong, Peiyun Xiao, Yongshou Yang, Chenggui Zhang, Zhengchun He

“…Concurrently, PA-011 activated the proliferative potential of hair follicle stem cells, as demonstrated by upregulated expression of the cell proliferation marker Ki67, and activated the Wnt/β-catenin signaling pathway in DHT-induced AGA mice. Transcriptomic and metabolomic analyses revealed multi-target effects of PA-011, including modulation of PI3K-Akt/MAPK pathways, pentose phosphate metabolism, and amino acid biosynthesis. 16S rRNA sequencing and metagenomic analysis showed that AGA disrupts skin microbial homeostasis, while PA-011 intervention normalized the microbiota composition. …”
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Transcriptome analyses of shell color and egg production traits between the uteruses of blue-green eggshell chickens and Hy-Line brown layers by Huanhuan Wang, Lei Zhang, Yinghui Wei, Hang Liu, Yanlu Wang, Ying Ge, Yuchun Pan

“…The up-regulated genes were CCR2, CCR8, CD40LG, IL18RAP, INHBA, and P2RY13, while the down-regulated genes were ABCA13, ADCY2, and GRM1. …”
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Identification and validation of m6A RNA methylation and ferroptosis-related biomarkers in sepsis: transcriptome combined with single-cell RNA sequencing by Jinshuai Lu, Jianhao Wang, Kun Han, Yuxia Tao, Jiyi Dong, Xiaoyu Pan, Xiaolan Wen

“…BackgroundSepsis, a systemic inflammatory response syndrome triggered by infection, is associated with high mortality rates and an increasing global incidence. While N6-methyladenosine (m6A) RNA methylation and ferroptosis are implicated in inflammatory diseases, their specific genes and mechanisms in sepsis remain unclear.MethodsTranscriptomic datasets of sepsis, along with m6A-related genes (m6A-RGs) and ferroptosis-related genes (FRGs), were sourced from public databases. …”
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Multi-omics integration reveals chromatin-associated lncRNA prognostic model in lung adenocarcinoma: Bridging GWAS, transcriptome and clinical outcomes by Xiao Zhu, Zhuolong Xiong

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LC/MS-based lipidomics and transcriptomics reveal lipid diversity and regulatory networks underlying intramuscular fat differences in Xingguo grey geese by Mengyun Zou, Weihong Zhang, Xiaolan Xiong, Linjie Rao, Qipeng Wei, Haiqin Li, Fanfan Zhang, Jinfang Xie, Zhangzhang Wang, Jiangnan Huang

“…To investigate the heterogeneity of IMF composition and its regulatory mechanisms in Xingguo (XG) geese with varying IMF levels, lipidomics and transcriptomics were utilized. The analysis of lipid profiles revealed that the predominant lipids in the IMF of XG geese were glycerophospholipids (GPs), followed by glycerides (GLs). …”
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Impact of dietary protein levels on growth, immune response, digestibility, intestinal microbiota, and transcriptome in Litopenaeus vannamei fed cottonseed protein concentrate by Hongming Wang, Xin Hu, Jian Chen, Yudong Zheng, Beiping Tan, Lili Shi, Shuang Zhang

“…Transcriptomic analysis identified significant signaling pathways affected by dietary treatments, notably the IL-17 signaling pathway, endoplasmic reticulum protein processing, and cholesterol metabolism. …”
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Transcriptomic Profiling of Heat-Treated Oriental Lily Reveals <i>LhERF109</i> as a Positive Regulator of Anthocyanin Accumulation by Mei Zhou, Lijia Zeng, Fan Li, Chunlian Jin, Jungang Zhu, Xue Yong, Mengxi Wu, Beibei Jiang, Yin Jia, Huijuan Yuan, Jihua Wang, Yuanzhi Pan

“…We subjected ‘Souvenir’ Oriental lily plants to temperature treatments (20 °C and 35 °C) and performed transcriptome sequencing and weighted gene co-expression network analysis (WGCNA). …”
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Metabolome and transcriptomics analyses reveal quality differences between Camellia tachangensis F. C. Zhang and C. sinensis (L.) O. Kunzte. by Yunfei Xu, Qihang Zhou, Xinglin Wang, Xingpan Meng, Zhengdong Zhang, Xu Zhang, Ximin Zhang, Suzhen Niu, Guiping Chen, Lunxian Liu, Tie Shen

“…Additionally, transcriptome analysis revealed 8049 differentially expressed genes, with 4418 upregulated and 3631 downregulated genes. …”
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Single-cell sequencing and transcriptomic data reveal that P65 activation significantly promotes microglia-mediated neuroinflammation after ischemic stroke by Ruiyu Wang, Yilun Qian, Xinchen Zhou, Hang Xu, Yu Wang, Yao Geng, Tianshu Wang, Binxiu Sha

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Dynamic metabolomic and transcriptomic profiling reveals yellow flower development in Camellia perpetua, a rare continuously flowering golden Camellia species by Xianliang Zhu, Haidu Jiang, Xinfeng Pan, Jiaxin Fu, Lihui Peng, Jin Zhang, Jianmin Tang, Rong Zou, Bo Zhao, Xiao Wei, Shengfeng Chai

“…Comparative transcriptomic profiling indicated that differentially expressed genes (DEGs) associated with photosynthesis were predominantly active during the early stages of flower development, while DEGs involved in the flavonoid biosynthesis pathway showed a marked increase as the flowers matured. …”
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Repetitive transcranial magnetic stimulation ameliorates chronic pain behavior and modulates the brain transcriptome in a mouse model of chronic constriction injury by Tianying Li, Guanwen Lin, Tao Zhang, Yani Guo, Yongjin He, Jing Luan, Jin Wang, Dan Lyu, Yiqi Weng, Xin Jin

“…Results and conclusion: rTMS at both 5 Hz and 10 Hz significantly improved PWL and PWT in CCI mice and reduced anxiety-like behaviors. Transcriptomic analysis revealed that CCI induced dysregulation of 66 genes, while rTMS partially normalized gene expression patterns. …”
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