Single-cell transcriptomic insights into endosulfan-induced liver injury: Key pathways and inflammatory responses by Pan Huang, Yunmeng Bai, Chaohua Zhou, Xiaoru Zhong, Ashok Iyaswamy, Peng Chen, Xu Wei, Wei Zhang, Chuanbin Yang, Jigang Wang

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Integrating transcriptomics and hybrid machine learning enables high-accuracy diagnostic modeling for nasopharyngeal carcinoma by Hehe Wang, Junge Zhang, Peng Cheng, Lujie Yu, Chunlin Li, Yaowen Wang

“…This study aimed to develop robust machine learning (ML)-driven diagnostic models and identify key biomarkers through integrated analysis of multi-cohort transcriptomic data. Methods Seven NPC transcriptomic datasets (GSE12452, GSE40290, GSE53819, and GSE64634 were merged to form the training cohort, while GSE13597, GSE34573, and GSE61218 served as independent external validation sets) were integrated and preprocessed using ComBat for batch effect correction. …”
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Pituitary Transcriptome Analysis of Genes and Pathways Related to Traits at the First Egg in Kangle Yellow Chicken by Jinge MA, Lan LAN, Zige LIU, Jiguo XU

“…RT-qPCR result showed that the expression trend of seven genes were consistent with transcriptome sequencing.【Conclusion】By analyzing the transcriptome sequencing results of the pituitary tissue of Kangle yellow Chicken, 12 candidate genes and 8 key gene pathways were screened, which provided solid data support for further exploring the molecular mechanism of regulating laying traits by the pituitary tissue genes in chicken.…”
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Comparative transcriptome and metabolome analysis of sweet potato (Ipomoea batatas (L.) Lam.) tuber development by Yanhui Lin, Yapeng Li, Yapeng Li, Honglin Zhu, Liqiong Tang, Jing Xu

“…A total of 14 candidate genes related to starch, carotenoids and anthocyanins in sweet potato tubers, including the IbCHI, IbUGP2 and IbglgA genes, were identified via weighted correlation network analysis (WGCNA).ConclusionThis research provides fresh insights into the levels of anthocyanins, starch, and carotenoids throughout the growth of sweet potato tubers and sheds light on the potential regulatory pathways and candidate genes involved in this developmental progression.…”
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The Causal Effects Between Circulating Inflammatory Proteins and Osteoarthritis: A Mendelian Randomization and Transcriptomic Analysis by Lin S, Wu C, Pan Y

“…Furthermore, this study used two transcriptomic cohorts from the GEO database to explore differentially expressed inflammation-related genes (IRGs) in OA and identify key inflammatory markers.Results: This study provides suggestive evidence. …”
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Identification and validation of pyroptosis-related genes in Alzheimer’s disease based on multi-transcriptome and machine learning by Yuntai Wang, Yuntai Wang, Yilin Li, Lu Zhou, Yihuan Yuan, Chuanfei Liu, Zimeng Zeng, Yuanqi Chen, Qi He, Zhuoze Wu

“…However, the molecular mechanisms through which pyroptosis-related genes (PRGs) drive AD pathogenesis remain incompletely elucidated.MethodsWe integrated multiple transcriptomes of AD patients from the GEO database and analyzed the expression of PRGs in combined datasets. …”
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Single-Cell Transcriptomic Analysis Unveils Key Regulators and Signaling Pathways in Lung Adenocarcinoma Progression by Jialu Ma, Caleb McQuay, John Talburt, Amit K. Tiwari, Mary Qu Yang

“…Single-cell RNA sequencing (scRNA-seq) technology has revolutionized our ability to dissect the cellular complexity of cancers, which is often obscured in conventional bulk transcriptomic experiments. <b>Methods:</b> In this study, we performed an integrative analysis of scRNA-seq data from multiple LUAD patient cohorts to investigate cell-type-specific transcriptomic changes across disease stages. …”
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Comparative transcriptome analysis reveals key genes and signaling pathways mediated by salicylic acid in potato by Aie Chen, Beini Zhang, Huijie Wang, Jiangqing Wang, Ji Wei, Yuxin Jia, Hongyang Wang

“…Conclusion This study provides a comprehensive overview of SA-responsive gene expression in potato, uncovering key regulatory components and pathways within the SA signaling network. …”
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Transcriptome Analysis of the Hippocampus in Domestic Laying Hens with Different Fear Responses to the Tonic Immobility Test by Jingyi Zhang, Min Li, Liying Pan, Ye Wang, Hui Yuan, Zhiwei Zhang, Chaochao Luo, Runxiang Zhang

“…This study investigated hippocampal histological characteristics and transcriptomic profiles in laying hens with different fear responses categorized based on TI duration. …”
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Transcriptomic and Metabolomic Analyses of the Piz-t-Mediated Resistance in Rice against <i>Magnaporthe oryzae</i> by Naeyeoung Choi, Xiao Xu, Pengfei Bai, Yanfang Liu, Shaoxing Dai, Matthew Bernier, Yun Lin, Yuese Ning, Joshua J. Blakeslee, Guo-Liang Wang

“…The gene expression patterns in the transcriptomic datasets were well correlated with the metabolomic profiling. …”
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Identification of Differentially Expressed Genes in the Hypothalamus of Broilers Under Heat Stress Using Transcriptome Analysis by Xiaofang He, Bingbing Ma, Lin Zhang, Feng Gao

“…Meanwhile, the anorexigenic part of pro-opiomelanocortin genes was up-regulated significantly in the HS group. The transcriptome sequencing results can help us understand the regulatory mechanism of feed intake decline in broilers under heat stress at the genetic level.…”
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Identifying candidate genes associated with hippocampal dysfunction in a hemiparkinsonian rat model by transcriptomic profiling by Bohye Kim, Sungmoo Hong, Jeongmin Lee, Sohi Kang, Joong-Sun Kim, Chaeyong Jung, Taekyun Shin, BuHyun Youn, Changjong Moon

“…STRING analysis confirmed a notable upregulation of eight hub genes (Notch3, Gng4, Itga3, Grin2d, Hgf, Fgf11, Htr3a, and Col6a2), along with a significant downregulation of two hub genes (Itga11 and Plp1), as validated by reverse transcription-quantitative polymerase chain reaction. This study provides a comprehensive transcriptomic profile of the hippocampi in a hemiparkinsonian rat model, thereby offering insights into the signaling pathways underlying hippocampal dysfunction.…”
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Transcriptomics, lipidomics, and single-nucleus RNA sequencing integration: exploring sphingolipids in MASH-HCC progression by Jing Zeng, Grayson Way, Nan Wu, Xixian Jiang, Yun-ling Tai, Derrick Zhao, Lianyong Su, Qianhua Yan, Xuan Wang, Emily C. Gurley, Phillip B. Hylemon, Sayed Obaidullah Aseem, Arun J. Sanyal, Jiangao Fan, Huiping Zhou

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Combined genome and transcriptome analysis identifies molecular signatures of aortic disease in patients with Marfan syndrome by Katherine B. Stanley, Alexa V. Mederos, Ethan H. Barksdale, Joel S. Corvera, Joshua L. Davis, Fang Fang, Hongyu Gao, Courtney E. Vujakovich, Yunlong Liu, Stephanie M. Ware, Benjamin J. Landis

“…In this study, we combine genome and transcriptome data from patients with MFS to determine the transcriptional impacts of disease-causing variants in FBN1. …”
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Transcriptome-based WGCNA reveals the molecular regulation of xylem plasticity in acclimation to drought and rewatering in mulberry by Yue Tian, Yue Tian, Zeyang Zhai, Zeyang Zhai, Yujie Yang, Yujie Yang, Kaixin Zhang, Kaixin Zhang, Sang Ma, Sang Ma, Jialing Cheng, Jialing Cheng, Li Liu, Li Liu, Xu Cao, Xu Cao

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Molecular landscape of atherosclerotic plaque progression: insights from proteomics, single-cell transcriptomics and genomics by Chaonan Wang, Yuyao Feng, Xiaoyan Liu, Haidan Sun, Zhengguang Guo, Jiang Shao, Kang Li, Junye Chen, Keqiang Shu, Deqiang Kong, Jiaxian Wang, Yiran Li, Xiangling Lei, Chen Li, Bao Liu, Wei Sun, Zhichao Lai

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Comparative transcriptomics analysis of the Oleidesulfovibrio alaskensis G20 biofilms grown on copper and polycarbonate surfaces by Priya Saxena, Dipayan Samanta, Payal Thakur, Vinoj Gopalakrishnan, Rajesh K. Sani

“…This study presents a comparative transcriptomic analysis of Oleidesulfovibrio alaskensis G20 biofilms grown on copper and polycarbonate surfaces, aimed at elucidating their differential responses at the molecular level. …”
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Mapping Small Extracellular Vesicle Secretion Potential in Healthy Human Gingiva Using Spatial Transcriptomics by Blanka Maria Borowiec, Małgorzata Blatkiewicz, Marta Dyszkiewicz-Konwińska, Dorota Bukowska, Bartosz Kempisty, Marcin Ruciński, Michał Nowicki, Joanna Budna-Tukan

“…In this study, we utilized spatial transcriptomics to map gene expression to specific spatial locations within the gingiva tissue section, using publicly available transcriptomic data. …”
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Temporal changes in the transcriptome profile of Macrobrachium rosenbergii in response to decapod iridescent virus 1 infection by Jingwen Hao, Jingwen Hao, Yukun Jie, Yukun Jie, Zhibin Lu, Zhibin Lu, Tiantian Ye, Jilun Meng, Cui Liu, Junjun Yan, Yutong Zheng, Zaijie Dong, Zhimin Gu

“…To gain deeper insights into the dynamic immune regulatory processes of M. rosenbergii in response to DIV1 infection, RNA sequencing (RNA-seq) was employed to profile the transcriptome in the hepatopancreas at 24, 48, 72, and 96 hours post-infection (hpi). …”
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Dynamic transcriptome and metabolome analyses of two sweet corn lines under artificial aging treatment by Zili Zhang, Ruichun Yang, Lei Gao, Shilin Huang, Feng Jiang, Qingchun Chen, Pengfei Liu, Faqiang Feng

“…The findings of this study are expected to provide valuable insights for the storage of sweet corn seeds.…”
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