Metagenomic and Transcriptomic Datasets of Plateau Brown Frogs (Rana kukunoris) from the Helan Mountains by Nan Zhang, Yao Zhao, Zhirong Zhang, Meiling Zhan, Xuyang Zhao, Yi Zhang, Jingyu Sun, Yuxuan Zhang, Liwei Teng, Zhensheng Liu

“…Therefore, this study investigates the adaptation strategies of the plateau brown frog to environmental changes, providing extensive transcriptomic and the first comprehensive metagenomic dataset from two distinctly different environmental regions (eastern and western slopes of the Helan Mountains). …”
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Exploring Migraine Pathogenesis: Transcriptomic Insights and Pathway Analysis in Nitroglycerin-Induced Rat Model by Qiao-Wen Chen, Run-Tian Meng, Chih-Yuan Ko

“…These findings suggest that migraine involves PI3K–Akt signaling and cytokine–cytokine receptor interactions, providing insights into molecular mechanisms and potential therapeutic targets. …”
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Unveiling the immune microenvironment of complex tissues and tumors in transcriptomics through a deconvolution approach by Shu-Hwa Chen, Bo-Yi Yu, Wen-Yu Kuo, Ya-Bo Lin, Sheng-Yao Su, Wei-Hsuan Chuang, I.-Hsuan Lu, Chung-Yen Lin

“…Additionally, mySORT outperforms existing methods like CIBERSORT in accuracy and provides a wide range of data visualization features, such as hierarchical clustering and cell complexity plots. …”
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A CRISPR/Cas9-based enhancement of high-throughput single-cell transcriptomics by Amitabh C. Pandey, Jon Bezney, Dante DeAscanis, Ethan B. Kirsch, Farin Ahmed, Austin Crinklaw, Kumari Sonal Choudhary, Tony Mandala, Jeffrey Deason, Jasmin S. Hamidi, Azeem Siddique, Sridhar Ranganathan, Keith Brown, Jon Armstrong, Steven Head, Phillip Ordoukhanian, Lars M. Steinmetz, Eric J. Topol

“…To address this challenge, here we introduce single-cell CRISPRclean (scCLEAN), a molecular method that globally recomposes scRNAseq libraries, providing a benefit that cannot be recapitulated with deeper sequencing. scCLEAN utilizes the programmability of CRISPR/Cas9 to target and remove less than 1% of the transcriptome while redistributing approximately half of reads, shifting the focus toward less abundant transcripts. …”
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Insight into the composition and differentiation of endophytic microbial communities in kernels via 368 maize transcriptomes by Fang Tao, Feng Chen, Haida Liu, Cheng Chen, Beijiu Cheng, Guomin Han

“…Conclusion: Tropical maize germplasm may have advantages in resisting the invasion of pathogenic microorganisms, providing excellent genetic resources for disease-resistant breeding.…”
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An atlas of immune cell exhaustion in HIV-infected individuals revealed by single-cell transcriptomics by Shaobo Wang, Qiong Zhang, Hui Hui, Kriti Agrawal, Maile Ann Young Karris, Tariq M. Rana

“…These data provide a comprehensive analysis of gene signatures associated with immune cell exhaustion during HIV infection, which could be useful in understanding exhaustion mechanisms and developing new cure therapies.…”
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Transcriptomic analysis reveals the mechanism underlying salinity-induced morphological changes in Skeletonema subsalsum by Jingwen Hu, Ya Zheng, Shuang Yang, Lin Yang, Lin Yang, Qingmin You, Quanxi Wang

“…Diatom cell walls are diverse and unique, providing the basis for species identification and supporting the ecological and economic value of diatoms. …”
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Unveiling alfalfa root rot resistance genes through an integrative GWAS and transcriptome study by Fei He, Ming Xu, Hao Liu, Yanchao Xu, Ruicai Long, Junmei Kang, Qingchuan Yang, Lin Chen

“…The integration of GWAS and RNA-Seq data identified four key DEGs associated with root rot resistance, providing valuable insights for breeding disease-resistant alfalfa varieties and enhancing crop resilience.…”
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Parallel measurement of transcriptomes and proteomes from same single cells using nanodroplet splitting by James M. Fulcher, Lye Meng Markillie, Hugh D. Mitchell, Sarah M. Williams, Kristin M. Engbrecht, David J. Degnan, Lisa M. Bramer, Ronald J. Moore, William B. Chrisler, Joshua Cantlon-Bruce, Johannes W. Bagnoli, Wei-Jun Qian, Anjali Seth, Ljiljana Paša-Tolić, Ying Zhu

“…Benchmarking of nanoSPLITS demonstrates high measurement precision with deep proteomic and transcriptomic profiling of single-cells. We apply nanoSPLITS to cyclin-dependent kinase 1 inhibited cells and found phospho-signaling events could be quantified alongside global protein and mRNA measurements, providing insights into cell cycle regulation. …”
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Transcriptomic analysis of theca cells in a PCOS rat model: insights into follicular development by Chen Yuanyuan, Sun Ningyu, Lu Lu, Zhang Wuwen, Li Kai, Li Yanting, He Junlan, Cheng Xiang, Zhou Jing, Yan Hua, Yin Ping

“…PCR validation confirmed that Cyp17a1, Cyp11a1, S6k1, mTOR, Akt, Kit, and Tek were significantly upregulated in the PCOS group (P < 0.05). Conclusion Transcriptomic analysis identified key genes and pathways involved in follicular development dysregulation in PCOS rats, providing potential targets for further research.…”
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Cross-tissue transcriptome-wide association study reveals novel psoriasis susceptibility genes by Fei Yan, Jing Tao, Jie Liu, Yongliang Chen, Zongju Huang

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Integrating transcriptomics and proteomics to analyze new regulatory genes related to rice grain development by Zhixuan Du, Qitao Su, Haihui Fu, Dahu Zhou, Linjuan Ouyang, Junru Fu, Haohua He

“…Furthermore, eight genes have been identified as potential regulators of grain development, providing valuable information on the underlying mechanisms of grain development in rice.To identify the key genes, pathways, and regulatory networks controlling rice grain size by integrating transcriptomic and proteomic analyses of large-grain (AD3) and small-grain (AD148) lines at critical developmental stages.…”
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Transcriptomic Divergence and Associated Markers Between Genomic Lineages of Silver Catfish (Rhamdia quelen) by Néstor Ríos, Belén G. Pardo, Carlos Fernández, José Antonio Alvarez‐Dios, Paulino Martínez, Carmen Bouza, Graciela García

“…In this study, we characterized the R. quelen transcriptome in brain, head kidney, liver, skeletal muscle, testis, and ovary by RNAseq to target genes and associated markers involved in key adaptive traits. …”
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Proteomic and transcriptomic analysis of the action mechanism of spermidine in mitigating the aging of Allium mongolicum seeds by Yan Men, Pengchao Wei, Xiumei Huang, Lu Yang, Zhenyu Cao, Jianting Wei, Xiaoyan Zhang, Fenglan Zhang, Zhongren Yang

“…Allium mongolicum seeds stored for different years were used to obtain germination indicators, physiological indicators, and proteomic and transcriptomic sequencing in seeds treated with spermidine (Spd). …”
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Phenotypic differences and transcriptomic analysis of extreme plant heights in a hybrid population of Hedychium by Xuanguo LIANG, Fang WANG, Yunyi YU, Yanping FAN

“…This study was aimed to identify key genes regulating plant height of Hedychium through phenotypic and transcriptome sequencing (RNA-seq) analyses, thereby providing an important reference basis for the molecular breeding and plant architecture improvement of Hedychium. …”
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Single-cell transcriptomics reveals the heterogeneity and function of mast cells in human ccRCC by Xiyu Song, Xiyu Song, Xiyu Song, Jianhua Jiao, Jianhua Jiao, Jiayang Qin, Wei Zhang, Weijun Qin, Weijun Qin, Shuaijun Ma, Shuaijun Ma

“…IntroductionThe role of mast cells (MCs) in clear cell renal carcinoma (ccRCC) is unclear, and comprehensive single-cell studies of ccRCC MCs have not yet been performed.MethodsTo investigate the heterogeneity and effects of MCs in ccRCC, we studied single-cell transcriptomes from four ccRCC patients, integrating both single-cell sequencing and bulk tissue sequencing data from online sequencing databases, followed by validation via spatial transcriptomics and multiplex immunohistochemistry (mIHC).ResultsWe identified four MC signature genes (TPSB2, TPSAB1, CPA3, and HPGDS). …”
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Transcriptomic analysis of melatonin on the mechanism of embryonic gonadal development in female Jilin white geese by Jin Yu, Ichraf Mabrouk, Qiuyuan Liu, Yuxuan Zhou, Yupu Song, Jingyun Ma, Fengshuo Liu, Xiangman Hu, Zhiyi Yang, Yuxia Zeng, Jingtao Hu, Yongfeng Sun

“…Furthermore, the findings offer valuable practical implications for the goose industry, providing professionals with scientifically grounded strategies to enhance reproductive efficiency and overall population productivity.…”
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Comprehensive Transcriptome Sequencing and Analysis of <i>Euspira gilva</i>: Insights into Aquaculture and Conservation by Zhixing Su, Jiayuan Xu, Xiaokang Lv, Xuefeng Song, Yanming Sui, Benjian Wang, Xiaoshan Wang, Bianbian Zhang, Baojun Tang, Liguo Yang

“…The findings of this research elucidate the full-length transcriptome profile of <i>E. gilva</i>, thereby establishing a foundational dataset and providing valuable insights for the species’ aquaculture, health management, conservation efforts, and future molecular biological investigations.…”
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Deciphering drought response mechanism in Tibetan qingke through comprehensive transcriptomic and physiological analysis by Deyuan Jiang, Deyuan Jiang, Shuaihao Chen, Shuaihao Chen, Shuaihao Chen, Zhongmengyi Qin, Zhongmengyi Qin, Zhongmengyi Qin, La Bo, La Bo, La Bo, Liping Niu, Liping Niu, Liping Niu, Hongkang Zhou, Hongkang Zhou, Jing Wang, Jing Wang, Jing Wang, Dawa Dondup, Xin Hou, Xin Hou, Xin Hou

“…This study conducted a comparative transcriptomic analysis of six qingke cultivars (three drought-tolerant and three drought-sensitive) under controlled drought conditions, with antioxidant enzyme activities monitoring. …”
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Genome-Scale DNA Methylome and Transcriptome Profiles of Prostate Cancer Recurrence After Prostatectomy by Jim Smith, Priyadarshana Ajithkumar, Emma J. Wilkinson, Atreyi Dutta, Sai Shyam Vasantharajan, Angela Yee, Gregory Gimenez, Rathan M. Subramaniam, Michael Lau, Amir D. Zarrabi, Euan J. Rodger, Aniruddha Chatterjee

“…Importantly, comprehensive clinical, histopathological, and follow-up data for each patient were provided to enable the correlation of transcriptome and methylome features with clinical features. …”
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