Enhanced fibrotic potential of COL1A1hiNR4A1low fibroblasts in ischemic heart revealed by transcriptional dynamics heterogeneity analysis at both bulk and single-cell levels by Cheng Luo, Cheng Luo, Cheng Luo, Baoping Tan, Luoxiang Chu, Liqiang Chen, Xinglong Zhong, Yangyang Jiang, Yuluan Yan, Fanrui Mo, Hong Wang, Fan Yang, Fan Yang

“…Cluster2 exhibited the highest gene activity in terms of fibrosis-related transcriptome dynamics. The characteristic gene expression profile of this FB subset indicated a specific upregulation of COL1A1 and several pro-fibrotic factors, including CCDC102B, GUCY1A3, TEX41, NREP, TCAP, and WISP, while showing a downregulation of NR4A1, an endogenous inhibitor of the TGF-β pathway. …”
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Genome-Wide Identification of Superoxide Dismutase (<i>SOD</i>) Gene Family in <i>Cymbidium</i> Species and Functional Analysis of <i>CsSOD</i>s Under Salt Stress in <i>Cymbidium s... by Ruyi Li, Songkun Lin, Yin Yan, Yuming Chen, Linying Wang, Yuzhen Zhou, Shuling Tang, Ning Liu

“…<i>Cis</i>-element prediction showed that stress-responsive elements were identified in most <i>SOD</i>s. Transcriptomic data revealed that seven <i>CsSOD</i>s exhibited a border expression in all sequenced tissues, while two exhibited undetectable expression levels. …”
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Identification of heat shock transcription factor gene families in sunflower and their expression profiles under abiotic stress(向日葵热激转录因子基因家族鉴定及其在非生物胁迫下的表达分析)... by 宋慧芳(SONG Huifang), 薛宏宇(XUE Hongyu), 王茜(WANG Xi), 卢俊洁(LU Junjie), 李晨雨(LI Chenyu), 刘阿克(LIU Ake)

“…Furthermore, the expression patterns of HaHSF genes were observed in various tissues and under hormone or abiotic stress conditions by analyzing transcriptome analysis. HaHSF12, HaHSF22, HaHSF27, and HaHSF33 showed responsiveness to exogenous plant hormones such as abscisic acid, salicylic acid; while HaHSF17, HaHSF18, and HaHSF33 might be involved in conferring abiotic stress resistance on sunflower seedlings. …”
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Distinct immune responses associated with vaccination status and protection outcomes after malaria challenge. by Damian A Oyong, Fergal J Duffy, Maxwell L Neal, Ying Du, Jason Carnes, Katharine V Schwedhelm, Nina Hertoghs, Seong-Hwan Jun, Helen Miller, John D Aitchison, Stephen C De Rosa, Evan W Newell, M Juliana McElrath, Suzanne M McDermott, Kenneth D Stuart

“…In-depth single-cell profiling of cell subsets that respond to CHMI in mock-vaccinated individuals showed a predominantly inflammatory transcriptome response. Whole blood transcriptome analysis revealed that gene sets associated with type I and II interferon and NK cell responses were increased in prior to CHMI while T and B cell signatures were decreased as early as one day following CHMI in protected vaccinees. …”
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A Survey of the ATP-Binding Cassette (ABC) Gene Superfamily in the Salmon Louse (Lepeophtheirus salmonis). by Greta Carmona-Antoñanzas, Stephen N Carmichael, Jan Heumann, John B Taggart, Karim Gharbi, James E Bron, Michaël Bekaert, Armin Sturm

“…Furthermore, some ABC transporters are recognised to be involved in conferral of insecticide resistance. While a number of studies have investigated ABC transporters in L. salmonis, no systematic analysis of the ABC gene family exists for this species. …”
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The Lyme disease bacterium, Borrelia burgdorferi, stimulates an inflammatory response in human choroid plexus epithelial cells. by Derick Thompson, Jordyn Sorenson, Jacob Greenmyer, Catherine A Brissette, John A Watt

“…These results were validated via RT-qPCR. Protein analysis of secreted factors showed an increase in inflammatory chemokines, corresponding to our transcriptome analysis. …”
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Interspecific Hybridization Enhanced Tolerance to Salinity and Cadmium Stress Through Modifying Biochemical, Physiological, and Resistance Gene Levels, Especially in Polyploid Rice... by Lixia Sun, Fozia Ghouri, Jiacheng Jin, Minghui Zhong, Weicong Huang, Zijun Lu, Jinwen Wu, Xiangdong Liu, Muhammad Qasim Shahid

“…Transcriptome analysis revealed that gene expression related to sugar metabolism processes increased in tetraploid hybrids. …”
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Fibro-adipogenic progenitor cells in skeletal muscle unloading: metabolic and functional impairments by Margarita Sorokina, Danila Bobkov, Natalia Khromova, Natalia Vilchinskaya, Boris Shenkman, Anna Kostareva, Renata Dmitrieva

“…Furthermore, C2C12 cultures treated with medium conditioned by FAPs showed diverse alterations: while the HS7 FAPs-derived paracrine factors supported the myoblasts fusion, the HS14-derived medium stimulated proliferation of C2C12 myoblasts; these observations were supported by increased expression of cytokines detected by transcriptome analysis. …”
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Understanding adaptation to fluconazole: comparative insights into tolerance and resistance in Saccharomyces cerevisiae and Candida albicans by Lijun Zheng, Yubo Dong, Jing Wang, Yonghui Jia, Weifang Wang, Yi Xu, Yi Xu, Liangsheng Guo

“…Chemical induction of petite formation led to an increase in resistance accompanied by a decrease in tolerance.ConclusionTranscriptome analysis indicated that petites up-regulated efflux mechanisms while down-regulating most ERG genes. …”
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Dynamics of the cell fate specifications during female gametophyte development in Arabidopsis. by Daichi Susaki, Takamasa Suzuki, Daisuke Maruyama, Minako Ueda, Tetsuya Higashiyama, Daisuke Kurihara

“…Here, we visualized the living dynamics of female gametophyte development and performed transcriptome analysis of individual cell types to assess the cell fate specifications in Arabidopsis thaliana. …”
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Post-transcriptional regulation in early cell fate commitment of germ layers by Rubens Gomes-Júnior, Cintia Delai da Silva Horinouchi, Aruana Fagundes Fiuza Hansel-Fröse, Annanda Lyra Ribeiro, Isabela Tiemy Pereira, Lucia Spangenberg, Bruno Dallagiovanna

“…By comparing these datasets, we identified genes subjected to post-transcriptional regulation in all germ layer differentiations and categorized the nature of this regulation. GO analysis demonstrated that polysome profiling serves as a complementary technique, capturing nuances that may be overlooked when analyzing only the transcriptome. …”
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Prediction of transcript isoforms and identification of tissue-specific genes in cucumber by Wenjiao Wang, Chengcheng Shen, Xinqiang Wen, Anqi Li, Qi Gao, Zhaoying Xu, Yuping Wei, Yushun Li, Dailu Guan, Bin Liu

“…Approximately 96.6% of these isoforms originated from known gene loci, while around 3.3% were derived from novel gene loci. …”
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Sucrose Promotes Strawberry Fruit Ripening and Affects Ripening-Related Processes by Ya Luo, Yuanxiu Lin, Fan Mo, Cong Ge, Leiyu Jiang, Yong Zhang, Qing Chen, Bo Sun, Yan Wang, Xiaorong Wang, Haoru Tang

“…It was suggested that 993 genes were differentially expressed comparing with the control. Transcriptome-based expression analysis revealed that sucrose induced the expression of genes involved in the AsA and anthocyanin biosynthesis, while largely suppressed the expression of genes in TCA. …”
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Overexpression of MMP14 is associated with poor prognosis and immune cell infiltration in colon cancer by Na Li, Nan Zhang, Guanghui Wang

“…MMP14 was overexpressed in CRC tissues and COLO205 cells. Single-cell transcriptome analysis revealed that MMP14 was highly expressed in fibrocyte cells within the liver metastasis group. …”
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Characteristics and Functions of Different Intestinal Segments in Juvenile Greater Amberjack (<i>Seriola dumerili</i>) by Kunfeng Zhu, Mouyan Jiang, Mengyao Yan, Yang Huang, Tonglin Yang, Chunhua Zhu

“…In this study, we divided the intestine of <i>S. dumerili</i> into foregut, midgut, and hindgut, and conducted a multi-omics analysis integrating histological staining (H&E/AB-PAS), digestive enzyme assays, transcriptome sequencing, and 16S rRNA microbiota profiling to characterize structural, functional, molecular, and microbial differences across intestinal segments. …”
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Exploring the longitudinal expression dynamics of midguts in adult female Amblyomma americanum ticks by Stephen Lu, Lucas C. de Sousa-Paula, Jose M. C. Ribeiro, Lucas Tirloni

“…Despite this, our overall understanding of tick midgut biology is limited. Results Our transcriptome analysis identified 15,599 putative DNA coding sequences (CDS), which were classified into 26 functional groups. …”
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The Cold Atmospheric Plasma Inhibits Cancer Proliferation Through Reducing Glutathione Synthesis by Qiyu Yang, Wei Zhao, Lingling Yang, Yongqin Fan, Changsheng Shao, Tao Wang, Fengqiu Zhang

“…., Retinoblastoma and Nuclear respiratory factor 2). Transcriptome analysis further explored molecular pathways involved in CAP-mediated anticancer effects. (3) Results: CAP reduced Glutaminase 1 and γ-glutamylcysteine ligase expression, leading to lower intracellular glutathione, higher ROS activity, and enhanced apoptosis. …”
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GINS1 facilitates the development of lung adenocarcinoma via Wnt/β-catenin activation by Luyuan Ma, Rongyang Li, Pengyong Li, Wenhao Yu, Zhanpeng Tang, Libo Si, Hui Tian

“…Methods Bioinformatic analysis including analysis of difference, survival analysis and pathway enrichment, immunohistochemistry(IHC), western blotting(WB), and quantitative real time polymerase chain reaction(qRT-PCR) were used to detect GINS1 expression in LUAD cell lines and tissues. …”
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Upregulation of IL-12 Signaling Genes Mediated by STAT4 Predicts a Complete Clinical Response in Patients with Squamous Cell Carcinoma of the Esophagus who Undergo Concurrent Chemo... by Nattida Sapsamarn, Asada Methasate, Pariyada Tanjak, Thanawat Suwatthanarak, Onchira Acharayothin, Kullanist Thanormjit, Jirawat Swangsri, Thammawat Parakonthun, Tetsuya Taga, Vitoon Chinswangwatanakul

“…Results: Of the 36 patients, 20 achieved cCR, while 16 had nonc-CR. Significant differences in immune transcriptomes were observed, particularly in IL-12 signaling mediated by STAT4. …”
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SMARCB1 orchestrates cellular plasticity and oncogenic pathways in typical and chondroid chordomas by Weihai Liu, Moksada Regmi, Shikun Liu, Ying Xiong, Yuwei Dai, Yingjie Wang, Jun Yang, Chenlong Yang

“…Functional studies revealed that SMARCB1 knockdown significantly enhanced cell proliferation, migration, and invasion. Transcriptome analysis demonstrated enrichment of MYC targets, E2F targets, and cell cycle pathways in SMARCB1-low samples, while cellular adhesion pathways were downregulated. …”
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