Comparative Analysis of Ratoon-Competent and Ratoon-Deficient Sugarcane by Hormonal and Transcriptome Profiling by Liping Zhao, Maoyong Ran, Jing Zhang, Peifang Zhao, Fenggang Zan, Jun Zhao, Wei Qin, Qibin Wu, Jiayong Liu, Xinlong Liu

“…Additionally, GT29 exhibited notable reductions in gibberellins (GA3 and GA5) and strigolactone (5-DS) post-stem-excision, while Badila displayed stable or distinct hormonal changes. …”
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Transcriptomic insights into the synergistic effects of darkness and mechanical stimulation on peanut pod development by Lu Huang, Muhammad J. Umer, Hao Liu, Haifen Li, Runfeng Wang, Qianxia Yu, Shaoxiong Li, Rajeev K. Varshney, Manish K. Pandey, Yanbin Hong, Qing Lu, Xiaoping Chen

“…These findings lay a foundation for exploring optimized growth conditions for peanut cultivation, while the identified key genes may serve as potential targets in future peanut breeding programs.…”
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Integrated transcriptomic analysis reveals evolutionary and developmental characteristics of tendon ossification in teleost by Xu-Dong Wang, Fei-Long Shi, Jia-Jia Zhou, Zheng-Yu Xiao, Tan Tu, Xue-Mei Xiong, Chun-Hong Nie, Shi-Ming Wan, Ze-Xia Gao

“…Results In this study, we systematically analyzed transcriptome data across multiple tissues, species, time points, and resolutions in teleosts. …”
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New insights into the transcriptomic profile during the late stages of chicken embryonic development by Di Zhao, Yifan Shi, Jiatai Deng, Bolin Zhong, Yuanyuan Zeng, Qingyuan Ouyang, Haihan Zhang, Zehe Song, Xi He

“…While comprehensive transcriptomic characterization of muscle development during the hatching stage remains limited, we conducted an integrated analysis of coding and non-coding RNA profiles in the pectoral muscles of Arbor Acres (AA) broilers and TaoYuan (TY) chickens at embryonic days 17 (E17), 19 (E19), and 21 (E21). …”
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Transcriptomic analysis of the toxic effects and potential mechanisms of fenvalerate on the liver of Odontobutis potamophila by Guoxing Liu, Tian Zhu, Zihan Zhou, You Zheng, Yanhua Zhao, Chen Hao, Shuyan Ding, Xiuhui Tan, Qichen Jiang

“…The results showed that FEN exposure caused tissue damage and oxidative stress in O. potamophila liver in a concentration-dependent manner. Transcriptomic analysis revealed 2083 differentially expressed genes (DEGs) between control (CK) and C0.5 treatments and 2595 DEGs between CK and C2 treatments. …”
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Transcriptome analysis reveals defense responses of alfalfa seedling roots to Sclerotium rolfsii by Shizhen Jia, Shizhen Jia, Zhencuo Dan, Zhencuo Dan, He Li, He Li, Yuhan Guo, Yuhan Guo, Lei Jia, Lei Jia, Ailing Yu, Ailing Yu, Huitong Zhan, Huitong Zhan, Xiangjun Liu, Xiangjun Liu, Teng Gao, Teng Gao, Yun Shi, Yun Shi, Zeng-Yu Wang, Zeng-Yu Wang, Lili Cong, Lili Cong, Lili Cong

“…Plant hormone signal transduction pathways exhibited the highest number of DEGs at 24 hpi, while plant-pathogen interaction pathways were dominant at 4 dpi. …”
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Bile acid synthesis, modulation, and dementia: A metabolomic, transcriptomic, and pharmacoepidemiologic study. by Vijay R Varma, Youjin Wang, Yang An, Sudhir Varma, Murat Bilgel, Jimit Doshi, Cristina Legido-Quigley, João C Delgado, Anup M Oommen, Jackson A Roberts, Dean F Wong, Christos Davatzikos, Susan M Resnick, Juan C Troncoso, Olga Pletnikova, Richard O'Brien, Eelko Hak, Brenda N Baak, Ruth Pfeiffer, Priyanka Baloni, Siamak Mohmoudiandehkordi, Kwangsik Nho, Rima Kaddurah-Daouk, David A Bennett, Shahinaz M Gadalla, Madhav Thambisetty

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Whole genome and transcriptome profiling in advanced pancreatic cancer patients on the COMPASS trial by Jennifer J. Knox, Gun Ho Jang, Robert C. Grant, Amy Zhang, Lucy Ma, Elena Elimova, Raymond Jang, Malcolm Moore, James Biagi, Mustapha Tehfe, Ravi Ramjeesingh, Erica S. Tsang, Spring Holter, Stephanie Ramotar, Shawn Hutchinson, Sheng-Ben Liang, Ilinca M. Lungu, Shari Moura, Yifan Wang, Sheron Perera, Michelle Chan-Seng-Yue, Maryam Monajemzadeh, Kyaw Aung, Rebecca Prince, Joan Miguel Romero, Jesus Fuentes-Antras, Galileo A. Gonzalez Conchas, Sarah Picardo, Ricardo Gonzalez, Sangeet Ghai, Korosh Khalili, Tae Kyoung Kim, Karen Ng, John Bartlett, Trevor J. Pugh, Sangeetha N. Kalimuthu, Sandra E. Fischer, Julie M. Wilson, Anna Dodd, George Zogopoulos, Barbara T. Grünwald, Faiyaz Notta, Steven Gallinger, Grainne M. O’Kane

“…Abstract Integrated whole genome and transcriptome sequencing can unveil distinct molecular subgroups in pancreatic cancer (PDAC). …”
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Translational and clinical comparison of whole genome and transcriptome to panel sequencing in precision oncology by Irina A. Kerle, Thomas Gross, Anja Kögler, Jonas S. Arnold, Maximilian Werner, Jan-Niklas Eckardt, Elena E. Möhrmann, Marie Arlt, Barbara Hutter, Jennifer Hüllein, Daniela Richter, Martin M. K. Schneider, Mario Hlevnjak, Lino Möhrmann, Dorothea Hanf, Christoph E. Heilig, Simon Kreutzfeldt, Maria-Veronica Teleanu, Evelin Schröck, Daniel Hübschmann, Peter Horak, Christoph Heining, Stefan Fröhling, Hanno Glimm

“…Our results showed that approximately half of the therapy recommendations (TRs) of both sequencing programs were identical, while approximately one-third of the TRs in WES/WGS ± TS relied on biomarkers not covered by the panel. …”
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Neoantigen-specific stimulation of tumor-infiltrating lymphocytes enables effective TCR isolation and expansion while preserving stem-like memory phenotypes by Yong Li, Steven A Rosenberg, Paul F Robbins, Zhiya Yu, Maria Parkhurst, Billel Gasmi, Nikolaos Zacharakis, Todd D Prickett, Jared J Gartner, Sri Krishna, Stephanie L Goff, Satyajit Ray, Frank J Lowery, Sivasish Sindiri, Alakesh Bera, Noam Levin, Sanghyun P Kim, Charles A Marquardt, Nolan R Vale, Lior Levy, Tiffany Benzine, Robert V Masi, Rafiqul Islam

“…Out of the 25 consecutive TIL samples, neoantigenic stimulation enabled the identification of 16 unique reactivities and 42 TCRs, while conventional TIL expansion identified 9 reactivities and 14 TCRs. …”
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Liver transcriptome response to avian pathogenic Escherichia coli infection in broilers with corticosterone treatment by Mengru Chen, Yifei He, Yimin Jia, Lei Wu, Ruqian Zhao

“…Liver transcriptomic analysis identified 768, 335, and 567 differentially expressed genes (DEGs) following CORT, APEC, or both treatments, respectively, enriched in cytokine-cytokine receptor interaction, PPAR signaling pathway, Toll-like receptor signaling pathway, MAPK signaling pathway, steroid hormone biosynthesis pathway, arachidonic acid metabolism, and phagosome pathway, etc., indicating that CORT treatment regulates lipid metabolism and immunity, while APEC infection induces inflammation and disrupts lipid metabolism. …”
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Decoding epithelial–fibroblast interactions in lung adenocarcinoma through single-cell and spatial transcriptomics by Jiajin Yang, Qiuping Xu, Yanjun Lu

“…Cell-cell communication was inferred via CellChat, while metabolic interactions were assessed using MEBOCOST. …”
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Integrated transcriptomics and metabolomics to explore the mechanisms of Elaeagnus mollis diels seed viability decline by Ren Ruifen, Guo Jiayi, Ji Zhe, Du Shuhui, Yang Xiuyun

“…Transcriptomic results showed that a total of 801 differentially expressed genes (DEGs) were identified between fresh and 1-month-stored seeds, while 1,524 were identified between fresh and 3-month-stored seeds. …”
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Comparative metabolome and transcriptome analysis of foxtail millet cultivars with high and low grain quality by Yiru Zhang, Xinjie Yao, Pengyu Tian, Canran Zhang, Xiaodong Liu, Hongying Li, Yuanhuai Han

“…These findings provide mechanistic insights into metabolic determinants of millet quality while establishing a framework for targeted breeding strategies to enhance both nutritional value and sensory characteristics in foxtail millet.…”
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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

“…Beneficial bacteria were predominant in the core species of networks in TST kernels, while pathogenic bacteria were more abundant in the core species of networks in NSS kernels. …”
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Transcriptome and detoxification enzyme–related gene analysis of the Cydia pomonella response to walnut husks by Xiaoyan Cao, Guangdong Li, Xiaoqin Ye, Adil Sattar

“…The results indicated that walnut husks trigger a stress response in C. pomonella larvae, while genes related to detoxification await further investigation. …”
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Spatial transcriptome analysis of myenteric plexus and intestinal epithelium of colon in patients with Parkinson’s disease by Chaewon Shin, Karoliina Eliisa Ruhno, Jung Hwan Shin, Sanha Hwang, Jasper Roldan Go, Minji Kang, Hyun Je Kim, Ji Hwan Moon, Han-Joon Kim

“…We performed spatial-specific transcriptomic profiling of the myenteric plexus and epithelium using the GeoMX Digital Spatial Profiler. …”
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In the battle of survival: transcriptome analysis of hypopharyngeal gland of the Apis mellifera under temperature-stress by Abdulkadir Yusif Maigoro, Jeong Hyeon Lee, Yumi Yun, Sujin Lee, Hyung Wook Kwon

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Combined metabolomic and transcriptomic analysis reveals the key genes for triterpenoid biosynthesis in Cyclocarya paliurus by Duo Chen, Xupeng Chen, Xuehai Zheng, Jinmao Zhu, Ting Xue

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An Integrative Analysis of the Transcriptome and Proteome of Rice Grain Chalkiness Formation Under High Temperature by Shaolu Zhao, Ruijie Cao, Linhe Sun, Dongying Zhuang, Min Zhong, Fengli Zhao, Guiai Jiao, Pengfei Chen, Xinwei Li, Yingqing Duan, Xiaoxue Li, Shaoqing Tang, Shen Ni, Peisong Hu, Xiangjin Wei

“…Grains under HT stress exhibited an opaque, milky-white appearance, alongside significant alterations in starch physicochemical properties. An integrated transcriptomic analysis of grains under HT revealed up-regulation of genes related to defense mechanisms and oxidoreductase activity, while genes involved in sucrose and starch synthesis were down-regulated, and α-amylase genes were up-regulated. …”
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