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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Transcriptome analysis reveals the sex-switching mechanism of juvenile hermaphroditism in silver pomfret (Pampus argenteus) by Yaya Li, Jiabao Hu, Chongyang Wang, Man Zhang, Youyi Zhang, Yuanbo Li, Mengke Tang, Chunlai Qin, Zukang Feng, Shanliang Xu, Xiaojun Yan, Xubo Wang, Haimin Chen, Yajun Wang

“…Candidate genes related to with sex differentiation were identified through differential gene expression analysis and feature selection methods, followed by gene set enrichment analysis to identify potential molecular pathways. …”
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Obesity impact on leukocyte telomere shortening and immune aging assessed by Mendelian randomization and transcriptomics analysis by Zhijun Feng, Jiacheng Li, Huimin Zhang, Shupeng Liu, Yinghui Wang, Meijuan Zhou, Zhenhua Ding, Lin Xiao

“…WHR had no significant causal relationship (P > 0.05). Transcriptomic analysis further revealed that individuals with obesity had higher expression of cellular senescence-related genes such as ID2, LMNA, and TENT4B in PBMCs compared to lean individuals, with expression levels of these genes significantly decreasing after bariatric surgery. …”
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Transcriptome analysis provides insights into aril development regulated gene network in lychee, longan, and rambutan by Suyan Wan, Fei Dong, Yaying Ma, Yuan Yao, Yang Wang, Yawen Xu, Ray Ming, Wenping Zhang

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Salinity tolerance in resting cysts of colpodid ciliates: Comparative transcriptomics analysis and chemical analysis of cyst walls to investigate their tolerance capability by Ryota Saito, Hiroki Yamanobe, Kazuma Yabuki, Tomohiro Suzuki, Takeru Saito, Shuntaro Hakozaki, Manfred Wanner, Ryota Koizumi, Tatsuya Sakai, Maribet Gamboa, Toshihiko Tanaka, Akiko Ono, Hoa Thanh Nguyen, Yuta Saito, Tetsuya Aoyama, Katsuhiko Kojima, Futoshi Suizu, Kozo Watanabe, Yoichiro Sogame

“…Colpoda resting cysts can tolerate saline conditions up to 3.5 % NaCl. A comparative transcriptome analysis of vegetative cells and resting cysts showed that the relative levels of expression of genes associated with membrane function increased in resting cysts. …”
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Transcriptomic analysis of melatonin-mediated drought stress response genes in alfalfa during germination period by Xiaoxia Zhang, Wenxuan Zhu, Zirui Liu, Xiangling Ren, Yingao Li, Guomin Li, Jingzhuo Wang, Xiaoyan Zhu, Yinghua Shi, Chengzhang Wang, Defeng Li, Hao Sun

“…To investigate the molecular mechanism underlying melatonin-mediated drought resistance in alfalfa, we performed a transcriptomic analysis on the seedlings. In the drought treatment group, we identified a total of 1,991 differentially expressed genes (DEGs), comprising 778 up-regulated and 1,213 down-regulated genes. …”
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Untargeted metabolomics and transcriptomics joint analysis of the effects of polystyrene nanoplastics on lipid metabolism in the mouse liver by Lijuan Chen, Guoyuan Sui, Jin Wu, Ning Li, Zhe Zhang, Ying Du, Meijun Lü, Xiaorui Yan, Guowei Pan, Lianqun Jia

“…Notably, NPs exposure induced opposing effects on serum lipid profiles, elevating high-density lipoprotein cholesterol (HDL-C) concentrations while suppressing triglyceride (TG) levels, though intergroup differences failed to reach statistical significance. (3) NPs caused multiple inflammatory responses in the liver, with significant lipid deposition. (4) Untargeted metabolomics analysis indicated that NPs exposure led to significant alterations in various lipid metabolites, particularly glycerophospholipids. …”
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Integrated metabolomic and transcriptomic analysis reveals the biosynthesis mechanism of dihydrochalcones in sweet tea (Lithocarpus litseifolius) by Shaojun Ling, Shaojun Ling, Shaojun Ling, Qiongqiong Lin, Qiongqiong Lin, Qiongqiong Lin, Biaofeng Zhou, Biaofeng Zhou, Biaofeng Zhou, Yiye Liang, Yiye Liang, Yiye Liang, Wenji Luo, Wenji Luo, Wenji Luo, Zhao Shen, Zhao Shen, Zhao Shen, Jingshu Wang, Jingshu Wang, Jingshu Wang, Jingwei Niu, Jingwei Niu, Jingwei Niu, Liangjing Qiao, Liangjing Qiao, Liangjing Qiao, Baosheng Wang, Baosheng Wang, Baosheng Wang, Hui Liu, Hui Liu, Hui Liu

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Changes of endogenous hormone concentrations and transcriptome analysis during the healing process of greenwood grafting in grape by DENG Jiayi, WEI Jiayan, CHEN Aisai, HE Fei, YU Keji, WANG Jun

“…Different stion combinations completed the healing process within 13 DAG. From the analysis of plant hormone levels, the concentration of IAA increased, while the concentrations of IP, ABA and JAs decreased during healing. …”
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Transcriptomic, and metabolic profiling reveals adaptive mechanisms of Auricularia heimuer to temperature stress by Chenhong Nie, Shiyan Wei, Shengjin Wu, Liangliang Qi, Jing Feng, Xiaoguo Wang

“…Here, we performed a comprehensive morphologic, transcriptomic, and metabolic analysis of A. heimuer mycelium exposed to different temperatures over a long period of time. …”
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Combined metabolome and transcriptome analysis revealed that MSTN regulated the process of bovine fatty acid metabolism in gut by Li Gao, Yong Ma, Lili Wang, Hao Wu, Ruobing Kang, Guangpeng Li, Lei Yang, Tong Wen

“…This study aims to reveal how MSTN affects the metabolism process by regulating gut metabolites.MethodsCombined analysis of jejunal contents metabolome and jejunal tissue transcriptome was used to compare the differences in intestinal metabolites and intestinal tissue gene expression between MSTN mutant and wild-type bovines.ResultsMetabolomic analysis identified that compared to wild-type bovine, the abundance of 304 metabolites were significantly changed in MSTN mutant cattle including 142 upregulated and 162 downregulated. …”
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ICARus: a pipeline to extract robust gene expression signatures from transcriptome datasets by Zhaorong Li, Juan I. Fuxman Bass, Juan I. Fuxman Bass, Juan I. Fuxman Bass, Juan I. Fuxman Bass

“…The ICARus package offers a robust pipeline to perform ICA on transcriptome datasets. While other packages perform ICA using one value of the main parameter (i.e., the number of signatures), ICARus identifies a range of near-optimal parameter values, iterates through these values, and assesses the robustness and reproducibility of the signature components identified. …”
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Elicitor-induced stilbene production and lignin reduction in peanut hairy roots: Insights from transcriptomic and metabolomic analysis by Apinun Limmongkon, Phadtraphorn Chayjarung, Chanyanut Pankaew, Sompop Pinit, Nitra Nuengchamnong, Chonnikan Tothong

“…Phenolic, flavonoid, and stilbene levels rose, while lignin content decreased over time. Transcriptomic analysis revealed upregulation of key genes in the phenylpropanoid pathway, including PAL, C4H, and 4CL, which correlated with elevated levels of hydroxybenzoic acid and related compounds. …”
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RNA-seq analysis of small intestine transcriptional changes induced by starvation stress in piglets by Yijia Ma, Tong Guo, Jianqin Ding, Zhiling Dong, Yifei Ren, Chang Lu, Yan Zhao, Xiaohong Guo, Guoqing Cao, Bugao Li, Pengfei Gao

“…In this study, we analysed the ileum of Large White (LW) and Mashen (MS) piglets at different times of starvation using chemical staining and transcriptome analysis. The intestinal barrier of piglets was damaged after starvation stress, but the intestinal antistress ability of MS piglets was stronger than LW piglets. …”
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Multi-omics analysis reveals the mechanism for galactose metabolism in mutant Streptococcus thermophilus IMAU20551Y by Jiahui Tai, Haimin Hu, Jinhui Liu, Wenhui Lu, Tong Dan

“…In this study, the ability of the mutant to metabolize galactose was verified by high performance liquid chromatography (HPLC), and the mechanism for enhanced galactose metabolism elucidated by multi-omics analysis. HPLC analysis showed that accumulation of galactose in milk fermented by mutant S. thermophilus IMAU20551Y was reduced by 41.4%, compared with the wild type. …”
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Cytological, Phytohormone, and Transcriptomic Analyses Reveal the Key Genes and Pathways Involved in Melon Fruit Cracking by Rong Fan, Bin Liu, Xiaoyu Duan, Meihua Li, Yongbing Zhang, Xuejun Zhang, Guozhi Hu, Yong Yang

“…This study investigated the pathways and genes related to melon fruit cracking through cell morphology observation, endogenous hormone analyses, and transcriptome analysis of two contrasting advanced inbred lines, the extremely crack-resistant line R2 and the crack-susceptible line R6. …”
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Advancing dimensionality reduction for enhanced visualization and clustering in single-cell transcriptomics by P. Sanju

“…These metrics collectively demonstrate CP-PaCMAP’s superior ability to retain meaningful biological patterns compared to other state-of-the-art dimensionality reduction techniques, making it an invaluable tool for advancing single-cell transcriptomic analysis.…”
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Oncogene-Induced Senescence Transcriptomes Signify Premalignant Colorectal Adenomas by Sofian Al Shboul, Heyam Awad, Anas Abu-Humaidan, Nidaa A. Ababneh, Ashraf I. Khasawneh, Tareq Saleh

“…Single-sample gene set enrichment analysis (ssGSEA) was performed to assess OIS and senescence-associated secretory phenotype (SASP) signatures, and differential gene expression analysis was conducted to examine key senescence-related genes. …”
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Transcriptome and hormonal analyses reveal an important role of auxin and cytokinin in regulating rice ratooning ability by Can Hu, Chenfan Zheng, Bo Liu, Like Sun, Jiaxi Yin, Yuanyuan Tan, Pedro García-Caparros, Qingyao Shu, Meng Jiang

“…Based on these findings, two high RA and one low RA varieties were selected for further analysis. Transcriptome sequencing was performed on these selected varieties, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. …”
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Temporal transcriptome and WGCNA analysis unveils divergent drought response strategies in wild and cultivated Solanum varieties by Athira C. Rajeev, Athira C. Rajeev, Rajesh Raju, Archana Pan

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