Combined Physiology and Transcriptome Analyses Provide Insights into Malformed Fruit of <i>Cocos nucifera</i> L. by Lilan Lu, Zhiguo Dong, Yuan Zhang, Siting Chen, Qingxin Wu

“…Transcriptomic dissection revealed 6370 functionally annotated differentially expressed genes (DEGs), comprising 4235 upregulated and 2135 downregulated transcripts. …”
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Transcriptomic, phenotypic and physiological analyses identify candidate regulators of Dendrobium stigma maturation and pollen-stigma interaction by Qian Wu, Shuxian Ren, Yuehong Ruan, Jiaxue Hu, Yin Li, Zongyan Li

“…Enzyme activities linked to stigma-pollen recognition—esterase, superoxide dismutase (SOD), and peroxidase (POD)—demonstrated stage-specific dynamics, with peak activity occurring during mid-anthesis (T2). Transcriptome analysis revealed that a total of 13,209 (T1), 12,557 (T2), and 18,593 (T3) Differentially expressed genes (DEGs) were identified, predominantly enriched in plant hormone signal transduction, MAPK signaling, and plant-pathogen interaction pathways. …”
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Integrated Analyses Reveal the Physiological and Molecular Mechanisms of Brassinolide in Modulating Salt Tolerance in Rice by Jia-Shuang Wu, De-Wei Mu, Nai-Jie Feng, Dian-Feng Zheng, Zhi-Yuan Sun, Aaqil Khan, Hang Zhou, Yi-Wen Song, Jia-Xin Liu, Jia-Qi Luo

“…The transcriptome analysis revealed that BR regulated the expression of 1042 and 826 genes linked to antioxidant activity, ion homeostasis, photosynthesis, and lipid metabolism under salt stress. …”
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Transcriptomics characteristics and differentiation of subcutaneous adipose tissue among Huainan pigs and its hybrid genetic populations by Taotao Yan, Taotao Yan, Mingyang Jia, Jiaxi Li, Xianyong Lan, Liwei Yuan, Baosong Xing, Chuanying Pan, Qingxia Lu, Jing Wang

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Single-Cell RNA Transcriptomics and Multi-omics Analyses Reveal the Clinical Effects of Acupuncture on Methadone Reduction by Yiming Chen, Baochao Fan, Jingchun Zeng, Yutian Zou, Chenyang Tao, Chen Chen, Peiming Zhang, Jian Liang, Fangfang Qi, Hailin Tang, Liming Lu

“…Therefore, we aimed to integrate clinical trial data with multi-omics analysis, including single-cell sequencing, transcriptomics, metabolomics, and metagenomics, to evaluate the effects of acupuncture in patients undergoing MMT. …”
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CD20, CTLA4, CXCL9, IL18RAP, IL-6, SOCS2, and TNF as potential biomarkers for rheumatoid arthritis disease progression: Systematic review of RNA-seq studies by Jairo Javier Jattin Balcázar, Daniel Felipe Galeano Sánchez, Gerardo Quintana López

“…Most biomarkers described were related to disease progression (61 %), while the most common analysis and tissue studied were principal component analysis (52 %) and blood (39 %), respectively. …”
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A deep insight into the sialome of the house fly, Musca domestica, infected with the salivary gland hypertrophy virus (MdSGHV) by Stephen Lu, Noa Miller, Adrian Wilson, Christopher J. Geden, John G. Stoffolano, Jose M. C. Ribeiro

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Two-Sample Mendelian Randomization Study Identifies Tissue-Dependent Risk Genes in Autoimmune Diseases by Ryan Chiu, Li Ma

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Transcriptional patterns of cancer-related genes in primary and metastatic tumours revealed by machine learning by Faeze Keshavarz-Rahaghi, Erin Pleasance, Steven J. M. Jones

“…Conclusions Our findings demonstrate the utility of machine learning in interpretation of cancer genomic data and provide new avenues for development of targeted therapies tailored to individual patients with cancer. Our analysis on the transcriptome revealed genes with expression levels strongly correlated with alterations in cancer-related genes. …”
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Effect of consuming blood-substitute feed on the transcriptome of the medicinal leech, Hirudo orientalis Utevsky and Trontelj, 2005 (Clitellata: Hirudinida) by Abbas Torabian, Majidreza Khoshkholgh, Sajad Nazari

“…While leeches in the genus Hirudo have long been models for neurobiology, the molecular underpinnings of nervous system structure and function in this group remain largely unknown. …”
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Potential threat of environmental toxin palytoxin to cerebral nerves: A mechanism study in vitro and in vivo by Xue Zhang, Lei Huang, Yinliang Liu, Xuewen Li, Huanying Zhou, Kang Qin, Shuang Li, Shuyue Ren, Xuexia Jia, Zhixian Gao

“…Furthermore, pretreatment with JNK and p38 inhibitors significantly restored mitochondrial membrane potential, ATP content, and cell viability, while reducing the expression of pro-apoptotic genes in HT22 cells. …”
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The archaeal class Nitrososphaeria is a key component of the reproductive microbiome in sponges during gametogenesis by Marta Turon, Vasiliki Koutsouveli, María Conejero, Sergi Taboada, Aida Verdes, José María Lorente-Sorolla, Cristina Díez-Vives, Ana Riesgo

“…Here, we use 16S rRNA gene analysis to assess whether the microbial composition of five gonochoristic sponge species differs between reproductive and non-reproductive individuals and correlate these changes with their gametogenic stages. …”
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Mitigating Cd stress in alfalfa: the role of melatonin and nano-calcium oxide in enhancing photosynthesis and antioxidant defense by Maqsood Ul Hussan, Umer Mahmood, Saeedeh Zarbakhsh, Sadam Hussain, Muhammad Bilal Hafeez, Noreen Zahra, Munib Ahmed, Quanzhen Wang, Mingke Yan

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Molecular evidence for the inverse comorbidity between central nervous system disorders and cancers detected by transcriptomic meta-analyses. by Kristina Ibáñez, César Boullosa, Rafael Tabarés-Seisdedos, Anaïs Baudot, Alfonso Valencia

“…We also observed expression deregulations in opposite directions at the level of pathways. Our analysis points to specific genes and pathways, the upregulation of which could increase the incidence of CNS disorders and simultaneously lower the risk of developing Cancer, while the downregulation of another set of genes and pathways could contribute to a decrease in the incidence of CNS disorders while increasing the Cancer risk. …”
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Desert-adapted tomato Solanum pennellii exhibit unique regulatory elements and stress-ready transcriptome patterns to drought. by J Sebastián Contreras-Riquelme, Miguel Contreras, Tomas C Moyano, Rachid Sjoberg, José Jimenez-Gomez, José M Alvarez

“…Through RNA-seq analysis, we identified orthologous genes between the two species and compared their transcriptomic profiles under both control and drought conditions. …”
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Distinctive chromosomal, mutational and transcriptional profiling in colon versus rectal cancers by Maria Teresa De Angelis, Antonia Rizzuto, Angela Amaddeo, Carlo Sagnelli, Niccolò Vono, Michela Reda, Valentina Lise, Luca Parrillo, Carmela De Marco, Donatella Malanga, Gianluca Santamaria, Giuseppe Viglietto

“…Methods We performed an integrated genomic and transcriptomic analysis of CC and RC data from The Cancer Genome Atlas (TCGA) to investigate their degree of similarity and observed that these tumors present distinct molecular profiles, which suggest an evolution through divergent pathways. …”
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Skin transcriptomic and selection signature analyses identify ASIP as a key gene in cattle coat color determination by Xin Wang, Longxin Xu, Di Zhou, Yanli Lv, Junda Wu, Yuanfeng Zhao, Mengmeng Ni, Wenzhang Zhou, Kaikai Zhang, Hua Wang, Jipan Zhang

“…Transcriptomic analysis identified 14,118 expressed genes, with principal component analysis and hierarchical clustering revealing clear differences between black and brown cattle. …”
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Nitrogen Deprivation Drives Red Motile Cell Formation in <i>Haematococcus pluvialis</i>: Physiological and Transcriptomic Insights by Hailiang Xing, Na Zhou, Kai Liu, Xiaotian Yan, Wanxia Li, Xue Sun, Liuquan Zhang, Fengjie Liu, Nianjun Xu, Chaoyang Hu

“…A transcriptomic analysis revealed substantial alterations in gene expression in response to ND. …”
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Integrated transcriptome and metabolome analyses provide molecular insights into the transition of flower color in the rose cultivar ‘Juicy Terrazza’ by Yun Xuan, Jie Ren, Zhu Chen, Dan Shi

“…In this study, the petal development of the rose cultivar ‘Juicy Terrazza’ was categorized into three stages: tangerine-colored petals in the flower bud (JT-T), orange-colored petals of the blooming flower (JT-O), and pink-colored petals of the open flower (JT-P). We utilized transcriptomics and metabolomics approaches to investigate the genes and metabolites involved in the pigment metabolic pathway across all three stages of rose petals (JT-T, JT-O, and JT-P) for transcriptomics analysis and two stages (JT-T and JT-P) for metabolomics analysis. …”
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Transcriptome and Metabolome Reveal Ferulic Acid as a Critical Phenylpropanoid for Drought Resistance in <i>Dendrobium sinense</i> by Huiyan You, Ao Yi, Qiongjian Ou, Jia Wang, Jun Niu

“…We then conducted the joint analysis of the metabolomics and transcriptomics data. …”
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