Single-cell and spatial transcriptome profiling reveal CTHRC1+ fibroblasts promote EMT through WNT5A signaling in colorectal cancer by Yunfei Lu, Yang Chen, Zhenling Wang, Hengyang Shen, Lei Xu, Changzhi Huang, Ying Tong, Yu Shao, Hongqiang Zhang, Zan Fu

“…Methods Single-cell RNA sequencing (scRNA-seq) technology was used to identify various cell subtypes. Spatial transcriptomics (ST) was employed to map the spatial niches and colocalization patterns of these cell subtypes. …”
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A Comparative Transcriptome Analysis Revealing the Mechanism Underlying the Effect of Maternal Plant Age on Adventitious Rooting of <i>Euryodendron excelsum</i> Cuttings by Ji Li, Xinyi Liu, Kunlin Wu, Shasha Wu, Junwen Zhai, Lin Fang, Songjun Zeng

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Unravelling the transcriptomic symphony of muscle ageing: key pathways and hub genes altered by ageing and caloric restriction in rat muscle revealed by RNA sequencing by Gulam Altab, Brian J. Merry, Charles W. Beckett, Priyanka Raina, Inês Lopes, Katarzyna Goljanek-Whysall, João Pedro de Magalhães

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Genome-Wide Transcriptome Analysis Reveals GRF Transcription Factors Involved in Methyl Jasmonate-Induced Flavonoid Biosynthesis in <i>Hedera helix</i> by Feixiong Zheng, Zhangting Xu, Xiaoji Deng, Xiaoyuan Wang, Yiming Sun, Xiaoxia Shen, Zhenming Yu

“…Notably, <i>HhGRF10</i> exhibited MeJA-induced expression that correlated temporally with flavonoid accumulation, suggesting that <i>HhGRF10</i> might play a potential role in promoting flavonoid biosynthesis, and overexpression and knockout assay substantiated this conclusion. The finding provides the first transcriptome-wide resource for flavonoid biosynthesis in <i>H. helix</i> and identifies the candidate GRF-mediated regulator for flavonoid accumulation.…”
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Single-cell transcriptomic analysis reveals the commonality of immune response upon H1N1 influenza virus infection in mice and humans by Yu Chen, Huaiyuan Cai, Qian Zhang, Gang Cao, Jiahao Zhang, Bing Yang, Jinxia Dai

“…The conserved immune mechanisms identified in this study provide potential therapeutic targets for enhancing antiviral immunity. …”
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Divergent molecular responsive mechanism of female and male spotted scat (Scatophagus argus) liver to 17β-estradiol revealed by the comparative transcriptome analysis by Xinyi Li, Shuhui Pan, Yun Zheng, Mingzhu Chen, Gang Shi, Guangli Li, Chunhua Zhu, Huapu Chen, Shangli Shi, Dongneng Jiang, Yucong Hong, Kaihui Sun, Hongjuan Shi

“…Transcriptome analysis identified 218, 1949, 548, and 1718 differentially expressed genes (DEGs) (FDR < 0.05 and |log2(FC)| ≥ 1) in livers of spotted scat across the Ctrl-ML vs. …”
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Combined analyses of mRNA and miRNA transcriptome reveal the molecular mechanisms of theca cells physiological differences in geese follicular selection stage by Xinyue Hu, Hengli Xie, Xi Zhang, Yueyue Lin, Shenqiang Hu, Jiwei Hu, Hua He, Liang Li, Hehe Liu, Jiwen Wang

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Mitochondrial oxidative phosphorylation (mtOXPHOS) serves as a sentinel to gauge fluctuations under heat stress in Arabidopsis thaliana elucidated by comparative transcriptomics by Muhammad Riaz, Erum Yasmeen, Moyang Liu, Hafiz Saqib Ali, Mengli Lv, Hu Shi, Chuanhui Du, Tiantian Dong, Zhenxin Liu, Qingwei Song, QiJun Ma, Kaijing Zuo

“…To analyze the molecular mechanism of the organelle's contribution to plant heat adaptation, we utilized publicly available transcriptomic datasets to identify the central module and key pathway responding to heat stress in Arabidopsis thaliana. …”
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Comparative transcriptome and defense hormone analyses of resistant and susceptible tea plant varieties revealed the response mechanisms of tea plants to Apolygus lucorum feeding by Yuan-Hong Wan, Chun Yang, Da-He Qiao, Yue-Xin Li, Xiao-Zeng Mi, Xing-Yun Shi, Shuai Li, Jin-Feng Zhang, Yu-He Wan, Ze-Hong Meng

“…Phenotypic evaluation revealed consistently less severe damage symptoms in TX0310 compared to HJY under identical infestation conditions. Through transcriptome sequencing approaches and integrated phytohormone profiling, we systematically elucidated the differential defense responses to A. lucorum. …”
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Deciphering mitochondrial dysfunction in keratoconus: Insights into ACSL4 from machine learning-based bulk and single-cell transcriptome analyses and experimental validation by Yuchen Cai, Tianyi Zhou, Xueyao Cai, Wenjun Shi, Hao Sun, Yao Fu

“…The identified pivotal biomarker ACSL4 provides a novel framework for future mechanistic and therapeutic studies of KC.…”
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Comparative transcriptomic analysis reveals a differential acid response mechanism between estuarine oyster (Crassostrea ariakensis) and Pacific oyster (Crassostrea gigas) by Shen-Tong Wang, Qi Yang, Ming-Kun Liu, Li Li, Wei Wang, Shou-Du Zhang, Guo-Fan Zhang

“…This study is the first to investigate acid-tolerance differences between mollusks inhabiting estuarine and open coastal environments and provides critical insights into the resilience of mollusks in increasingly acidified oceans.…”
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Comprehensive Metabolomic and Transcriptomic Analysis Revealed the Molecular Basis of the Effects of Different Refrigeration Durations on the Metabolism of <i>Agaricus bisporus</i>... by Zhixin Cai, Zhiheng Zeng, Wenzhi Chen, Zhongjie Guo, Huiqing Zheng, Yuanping Lu, Hui Zeng, Meiyuan Chen

“…Two CCMs (ketoleucine and 3-methyl-2-oxovaleric acid) gradually decreased in expression, whereas two CCGs (AbbBCAT and AbbAACS) increased in expression. This study provides novel insights into the molecular adaptation of <i>A. bisporus</i> spawn to refrigeration, highlighting the importance of branched-chain amino acid metabolism in the cold stress response and storage stability.…”
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SIGLEC1 has the potential to be an immune-related prognostic indicator in colon adenocarcinoma: a study based on transcriptomic data and Mendelian randomization analysis by Jue Gu, Yaxuan Wang, Hui Zhang, Haijuan Gu, Haixia Zhu

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Integrative lipidomic and transcriptomic analysis unraveled polystyrene nanoplastics-induced liver injury via oral and inhalation exposure: All roads lead to Rome? by Yiling Ge, Sheng Yang, Tianyi Zhang, Jie Li, Saisai Gong, Yifei Fang, Yuting Liang, Lihong Yin, Yuepu Pu, Zaozao Chen, Geyu Liang

“…Multidimensional assessments revealed exposure route-specific pathological patterns: oral administration primarily caused histopathological damage, whereas inhalation exposure induced more severe hepatic synthetic impairment and systemic inflammatory responses. Transcriptomic profiling identified 739 and 1350 differentially expressed genes (DEGs) for oral and inhalation routes respectively, with merely 17% overlap (228 DEGs), demonstrating fundamentally distinct molecular responses. …”
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Whole blood transcriptome profiles of trypanotolerant and trypanosusceptible cattle highlight a differential modulation of metabolism and immune response during infection by Trypan... by Peylhard, Moana, Berthier, David, Dayo, Guiguigbaza-Kossigan, Chantal, Isabelle, Sylla, Souleymane, Nidelet, Sabine, Dubois, Emeric, Martin, Guillaume, Sempéré, Guilhem, Flori, Laurence, Thévenon, Sophie

“…Overall, this study provides a better understanding of the biological mechanisms at work during infection, especially concerning the interplay between immunity and metabolism that seems differentially regulated depending on the cattle breeds. …”
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Quorum Sensing in <i>Chromobacterium subtsugae</i> ATCC 31532 (Formerly <i>Chromobacterium violaceum</i> ATCC 31532): Transcriptomic and Genomic Analyses by Dmitry G. Deryabin, Ksenia S. Inchagova, Eugenia R. Nikonorova, Ilshat F. Karimov, Galimzhan K. Duskaev

“…The goal of this study is to conduct transcriptomic and genomic analyses of the <i>C. subtsugae</i> ATCC 31532 (formerly <i>C. violaceum</i> ATCC 31532) strain to identify density-dependent regulated genes and the mechanisms of their QS control. …”
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Preliminary Analysis of the Formation Mechanism of Floret Color in Broccoli (<i>Brassica oleracea L var. italica</i>) Based on Transcriptomics and Targeted Metabolomics by Qingqing Shao, Mindong Chen, Saichuan Cheng, Huangfang Lin, Biying Lin, Honghui Lin, Jianting Liu, Haisheng Zhu

“…The color difference and pigment content of florets were measured, and a combined analysis of anthocyanin-targeted metabolome and transcriptome was conducted. Our findings revealed that chlorophyll a primarily influences green, yellow-green, and light green coloration, while the wax content may contribute to gray-green coloration. …”
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Genome-wide and transcriptome analysis of PdWRKY transcription factors in date palm (Phoenix dactylifera) revealing insights into heat and drought stress tolerance by Ibrahim Khan, Lubna, Saqib Bilal, Ashraf M. M. Abdelbacki, Sang-Mo Kang, Ahmed AL-Harrasi, Sajjad Asaf, In-Jung Lee

“…Abstract Genomic and transcriptomic studies on date palm (Phoenix dactylifera) are still inadequate, but several studies have contributed to understanding its genetic makeup, especially in the Khalas cultivar. …”
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Transcriptomic characterization of GMP-compliant regulatory macrophages (TRI-001) under inflammatory and hypoxic conditions: a comparative analysis across macrophage subtypes by Karina Zitta, Rouven Berndt, Katharina Hess, Fred Fändrich, Olga Gurvich, Katja Sirviö, Tuija Kekarainen, Lars Hummitzsch, Yuk Lung Wong, Ole Sattler, Steven Braem, Mark Krebs, Axel Fudickar, Sibille Engels, Nicole Flack, Markus Steinfath, Martin Albrecht

“…Aim of the Study To compare the transcriptome of TRI-001 with various in vitro differentiated macrophage subtypes to provide a comprehensive context for TRI-001 within the macrophage landscape. …”
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Single-nucleus transcriptomics reveals a distinct microglial state and increased MSR1-mediated phagocytosis as common features across dementia subtypes by Sook-Yoong Chia, Mengwei Li, Zhihong Li, Haitao Tu, Jolene Wei Ling Lee, Lifeng Qiu, Jingjing Ling, Richard Reynolds, Salvatore Albani, Eng-King Tan, Adeline Su Lyn Ng, Jinmiao Chen, Li Zeng

“…While these subtypes share clinical, genetic, and pathological features, their transcriptomic similarities and differences remain poorly understood. …”
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