Effects of purple corn anthocyanin on slaughter performance, immune function, the caecal microbiota and the transcriptome in chickens by Xingzhou Tian, Chao Ban, Di Zhou, Hui Li, Jiaxuan Li, Xu Wang, Qi Lu

“…The slaughter performance and caecal short-chain fatty acid parameters did not differ (P > 0.05) between the PCE and CON groups. …”
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The single-cell transcription reveals the aberrant differentiation trajectory of chondrocytes in the intervertebral disc for congenital scoliosis by Junfeng Wang, Haodong Li, Dong Fu, Yiming Zheng, Chuang Qian, Lin Li, Maoxiang Qian, Dahui Wang

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Cross modality learning of cell painting and transcriptomics data improves mechanism of action clustering and bioactivity modelling by Son V. Ha, Steffen Jaensch, Maciej M. Kańduła, Dorota Herman, Paul Czodrowski, Hugo Ceulemans

“…While multimodal learning of chemical structure-cell painting, or different omics data has been experimented; a cell painting-bulk transcriptomics multimodal model is still unexplored. …”
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Transcriptomic dynamics and cell-to-cell communication during the transition of prospermatogonia to spermatogonia revealed at single-cell resolution by Zhen He, Rong-Ge Yan, Qin-Bang Shang, Qi-En Yang

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Transcriptomic analysis of the 12 major human breast cell types reveals mechanisms of cell and tissue function. by Katelyn Del Toro, Rosalyn Sayaman, Kate Thi, Yamhilette Licon-Munoz, William Curtis Hines

“…Unfortunately, the complexity of tissues often hinders our ability to distinguish between neighboring cell types and, in turn, scrutinize their transcriptomes and generate reliable and tractable cell models for studying their inherently different biologies. …”
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spliceJAC: transition genes and state‐specific gene regulation from single‐cell transcriptome data by Federico Bocci, Peijie Zhou, Qing Nie

“…Abstract Extracting dynamical information from single‐cell transcriptomics is a novel task with the promise to advance our understanding of cell state transition and interactions between genes. …”
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Adaptive Resistance of <i>Staphylococcus aureus</i> to Cefquinome Sulfate in an In Vitro Pharmacokinetic Model with Transcriptomic Insights by Yue Hu, Hao Zhu, Xingbo Zhang, Yuhui Wu, Jingtao Li, Nan Li, Zhanbo Cai, Yuhui Yang

“…Experiments were conducted to investigate the pattern of adaptive resistance of <i>S. aureus</i> to cefquinome sulfate under different dosage regimens by using pharmacokinetic-pharmacodynamics (PK-PD) modeling, and the adaptive-resistant bacteria in different states were screened and subjected to transcriptomic sequencing. …”
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The important role of cuproptosis and cuproptosis-related genes in the development of thyroid carcinoma revealed by transcriptomic analysis and experiments by Yani Liu, Yanyan He, Shizhen Lei

“…For transcriptomic analysis, the transcriptomic data of THCA (n = 493) and normal thyroid samples (n = 58) was used. …”
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Insights into the strategy of micro-environmental adaptation: Transcriptomic analysis of two alvinocaridid shrimps at a hydrothermal vent. by Fang-Chao Zhu, Jin Sun, Guo-Yong Yan, Jiao-Mei Huang, Chong Chen, Li-Sheng He

“…Two alvinocaridid shrimps, Alvinocaris longirostris and Shinkaicaris leurokolos occupy distinct microhabitats around these vents and exhibit different thermal preferences. S. leurokolos inhabits the central area closer to the active chimney, while A. longirostris inhabits the peripheral area. …”
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Spatial transcriptomics and scRNA-seq: decoding tumor complexity and constructing prognostic models in colorectal cancer by Wei Song, Yatao Wang, Min Zhou, Fengqin Guo, Yanliang Liu

“…Abstract Introduction Recent advancements in transcriptomic analysis, combined with single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics, have deepened our understanding of the tumor microenvironment and cellular heterogeneity, laying the groundwork for personalized therapies. …”
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Transcriptome enhanced rice grain metabolic model identifies histidine level as a marker for grain chalkiness by Niaz Bahar Chowdhury, Anil Kumar Nalini Chandran, Harkamal Walia, Rajib Saha

“…For this, we reconstructed the rice grain genome-scale metabolic model (GSM), iOSA3474-G and incorporated transcriptomics data from three different times of the day (dawn, dawn 7 h, and dusk) for both control and WNT conditions with iOSA3474-G. …”
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High-throughput sequencing and de novo assembly of Brassica oleracea var. Capitata L. for transcriptome analysis. by Hyun A Kim, Chan Ju Lim, Sangmi Kim, Jun Kyoung Choe, Sung-Hwan Jo, Namkwon Baek, Suk-Yoon Kwon

“…The sequencing data from this study can be used to develop molecular markers and to identify the extreme differences among the phenotypes of different species in the genus Brassica.…”
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Integrated transcriptome and metabolome analyses reveal the differentially expressed metabolites and genes involved in lipid in olive fruits by Jipeng Qu, Zhou Xu, Zhengsong Peng, Zhenyong Chen, Tao Chen, Chunbang Ding

“…This study provides a strong theoretical and experimental foundation for further revealing the molecular mechanisms regulating lipid synthesis and metabolism in different olive cultivars.…”
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Characteristics of immune-active and immune-silent phenotypes of early-stage cervical carcinoma as revealed by transcriptome sequencing by O. V. Kurmyshkina, P. I. Kovchur, T. O. Volkova

“…PREDA demonstrated that these transcriptomic differences could be linked to different chromosomal regions and co-localized with particular gene families and potentially the reported virus integration hotspots. …”
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Transcriptomic profiling of gastrointestinal tracts in dairy cattle during lactation reveals molecular adaptations for milk synthesis by Yahui Gao, George E. Liu, Li Ma, Lingzhao Fang, Cong-jun Li, Ransom L. Baldwin, VI

“…We analyzed 27,607 gene expression patterns at multiple periods, enabling direct comparisons within and among tissues during different lactation stages, including early and peak lactation. …”
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Revealing the Molecular Regulatory Mechanism of Flavonoid Accumulation in Tender Leaves of Tea Plants by Transcriptomic and Metabolomic Analyses by Ruiyang Shan, Yongheng Zhang, Xiaomei You, Xiangrui Kong, Yazhen Zhang, Xinlei Li, Lu Wang, Xinchao Wang, Changsong Chen

“…Research has shown that the abundance of flavonoid glycosides varies greatly among different cultivars, but research on the regulatory mechanisms that cause their differential accumulation among tea plant cultivars with different leaf colors is lacking. …”
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A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways. by Martín Garrido-Rodriguez, Daniel Lopez-Lopez, Francisco M Ortuno, María Peña-Chilet, Eduardo Muñoz, Marco A Calzado, Joaquin Dopazo

“…MIGNON covers the whole process, from reads to signaling circuit activity estimations, using state-of-the-art tools, it is easy to use and it is deployable in different computational environments, allowing an optimized use of the resources available.…”
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Multi-omics analysis reveals associations between gut microbiota and host transcriptome in colon cancer patients by Yuling Qin, Qiang Wang, Qiumei Lin, Fengfei Liu, Xiaolan Pan, Caibiao Wei, Junxian Chen, Taijun Huang, Min Fang, Weilong Yang, Linghui Pan

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Single cell transcriptomics correlate avian coronavirus prime vaccination efficacy with antigen-presenting cell preference by Xuefeng Li, Yumeng Liang, Yu Zhang, Botao Fa, Zheyi Liu, Lu Cui, Miaomiao Xi, Shufeng Feng, Li Xu, Xiaoxiao Liu, Zhengtao Xiao, Shengwang Liu, Hai Li

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Spatial transcriptomics reveals unique metabolic profile and key oncogenic regulators of cervical squamous cell carcinoma by Limin Zhou, Jiejie Liu, Peipei Yao, Xing Liu, Fei Chen, Yu Chen, Li Zhou, Chao Shen, You Zhou, Xin Du, Junbo Hu

“…To delve deeper into the understanding of CSCC development, our research focused on analyzing the tumor microenvironment and metabolic characteristics across different regions of tumor tissue. Methods Utilizing spatial transcriptomics (ST) sequencing technology, we conducted a study on FFPE (formalin-fixed paraffin-embedded) tumor samples from CSCC patients. …”
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