Integrated transcriptome and proteome analysis identifies keratins as key regulators of corneal scarring in a murine model by Tianyi Zhou, Yuchen Cai, Fei Fang, Xueyao Cai, Yao Fu

“…A surgical model of stromal injury was established, and corneal tissue was harvested 3 weeks post-wounding and subjected to RNA sequencing and tandem mass tag proteomics. …”
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Integrated transcriptomic and microbiomic analyses reveal mechanisms of Decapod iridescent virus 1 resistance in Macrobrachium rosenbergii by Jingwen Hao, Jingwen Hao, Yukun Jie, Yukun Jie, Zhibin Lu, Zhibin Lu, Tiantian Ye, Jilun Meng, Cui Liu, Junjun Yan, Yutong Zheng, Zaijie Dong, Zhimin Gu

“…Hepatopancreas transcriptomic (RNA-Seq) and gut microbiome analyses were conducted on samples at 0, 24, and 48 hours post-infection (hpi) from both families. …”
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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

“…O-GlcNAc glycosylation was detected in the stigma transcriptome for the first time, potentially linked to kinase activity and immune responses. …”
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Genome-scale mRNA and miRNA transcriptomic insights into the regulatory mechanism of cucumber corolla opening by Xiao-fei SONG, Dan-feng GE, Yang XIE, Xiao-li LI, Cheng-zhen SUN, Hao-nan CUI, Xue-yun ZHU, Ren-yi LIU, Li-ying YAN

“…This integrated study on the transcriptional and post-transcriptional profiles can provide insights into the molecular regulatory mechanism underlying corolla opening in the cucumber.…”
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Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast. by Emanuel Gonçalves, Zrinka Raguz Nakic, Mattia Zampieri, Omar Wagih, David Ochoa, Uwe Sauer, Pedro Beltrao, Julio Saez-Rodriguez

“…Cells react to extracellular perturbations with complex and intertwined responses. Systematic identification of the regulatory mechanisms that control these responses is still a challenge and requires tailored analyses integrating different types of molecular data. …”
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Transcriptomic Profiling of Virus-Host Cell Interactions following Chicken Anaemia Virus (CAV) Infection in an In Vivo Model. by Efstathios S Giotis, Lisa Rothwell, Alistair Scott, Tuanjun Hu, Richard Talbot, Daniel Todd, David W Burt, Elizabeth J Glass, Pete Kaiser

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Transcriptomic landscape around wound bed defines regenerative versus non-regenerative outcomes in mouse digit amputation. by Archana Prabahar, Connie S Chamberlain, Ray Vanderby, William L Murphy, William Dangelo, Kulkarni Mangesh, Bryan Brown, Barsanjit Mazumder, Stephen Badylak, Peng Jiang

“…Additionally, we developed a deep learning AI model capable of predicting post-amputation time and level from RNA-seq data, indicating that the regenerative probability may be "encoded" in the transcriptomic response to amputation.…”
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Transcriptomic and histological characteristics of innate immune activation in brain parenchyma in a rat model of neonatal intraventricular hemorrhage by Miriam Zamorano, Sanjna Udtha, Aidan M. Collier, Erica Underwood, Razan El Sayed, Ankit Agarwal, Devin S. Hatchell, Chunfeng Tan, Paul J. Nietert, Scott D. Olson, Brandon A. Miller

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Transcriptome profiling of L. infantum-infected human macrophages reveals sex-specific type I interferon induction. by Annika Bea, Helena Fehling, Fabian Hausmann, Fahten Margot Habib, Melanie Lütkemeyer, Lara Buer, Carola Schäfer, Charlotte Sophie Hansen, Barbara Honecker, Stefan Bonn, Bianca Elisabeth Schneider, Joachim Clos, Hanna Lotter

“…Leishmania parasites infect and proliferate in innate immune cells, particularly macrophages, and modulate early immune responses that constrain their survival and replication. …”
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Transcriptomic and metabolomic analyses reveal molecular mechanisms of tobacco mosaic virus (TMV) resistance in Nicotiana tabacum L. by Caiyue Li, Qiang Zhang, Xuebo Wang, Zhengwen Liu, Xinyao Zhang, Caihong Jiang, Lirui Cheng, Aiguo Yang, Yangyang Li, Yan Ji, Dan Liu

“…Transcriptomic analysis revealed that the number of differentially expressed genes (DEGs) in R_K326 was about 2 times higher than in K326 at 9 days post-inoculation (dpi), suggesting a greater involvement of defense-related genes in the resistant line. …”
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Integrating transcriptomic and proteomic analyses of photoperiod-sensitive in near isogenic maize line under long-day conditions by Xiao-heng SONG, Lei TIAN, Shun-xi WANG, Jin-long ZHOU, Jun ZHANG, Zan CHEN, Liu-ji WU, Li-xia KU, Yan-hui CHEN

“…By integrating RNA-based transcriptomic and iTRAQ LC-MS/MS-based proteomic approaches, we generated a comprehensive inventory of the transcripts and proteins with altered abundances in response to a long photoperiod (LP) during growth stage transitions. …”
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Long-lasting sex-specific alteration in left ventricular cardiac transcriptome following gamma and simGCRsim radiation by Roksana Zakharyan, Siras Hakobyan, Agnieszka Brojakowska, Suren Davitavyan, Ani Stepanyan, Tamara Sirunyan, Gisane Khachatryan, Mary K. Khlgatian, Malik Bisserier, Shihong Zhang, Susmita Sahoo, Lahouaria Hadri, Venkata Naga Srikanth Garikipati, Arsen Arakelyan, David A. Goukassian

“…SimGCRsim-IR showed more persistent transcriptome changes than γ-IR. We suggest that the single IR effects can persist up to 550–660 days, with overwhelmingly sex-biased responses at individual gene expression level.…”
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Root Transcriptome Analysis Identifies Salt-Tolerance Genes in Sweet Corn Chromosome Segment Substitution Lines (CSSLs) by Zili Zhang, Xuxuan Duan, Pengfei Liu, Qingchun Chen, Wei Sun, Xiaorong Wan, Yixiong Zheng, Jianting Lin, Feng Jiang, Faqiang Feng

“…We conducted comparative phenotyping and physiological profiling of seedlings under salinity treatment, and transcriptome analysis was carried out by sampling root tissues at 0 h, 4 h, 12 h, and 72 h post-treatment. …”
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An integrated transcriptomic and metabolomic analysis of black spot disease in Jinggang honey pomelo reveals underlying resistance mechanisms by Huimin Sun, Weiwei Li, Lin Lu, Biling Jin, Dingkun Liu, Zexia Li, Li He, Yang Wu

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Identification of potential biomarkers for 2022 Mpox virus infection: a transcriptomic network analysis and machine learning approach by Joy Prokash Debnath, Kabir Hossen, Sabrina Bintay Sayed, Md. Sayeam Khandaker, Preonath Chondrow Dev, Saifuddin Sarker, Tanvir Hossain

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Integrative GWAS and transcriptomics reveal GhAMT2 as a key regulator of cotton resistance to Verticillium wilt by Long Wang, Long Wang, Long Wang, Yonglin Yang, Jianghong Qin, Qifeng Ma, Kaikai Qiao, Shuli Fan, Yanying Qu

“…Transcriptomic profiling revealed that GhAMT2 was significantly upregulated at 12 hours post-inoculation with V. dahliae, coinciding with the activation of immune signaling pathways. …”
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Single-cell transcriptome analysis revealed a suppressive tumor immune microenvironment in EGFR mutant lung adenocarcinoma by Lei Yang, Qing Zhou, Bo Zhang, Yi-Long Wu, Zhi-Hong Chen, Wen-zhao Zhong, Fen Wang, Yun-Ting He, Song Dong, Xue-Wu Wei, Wei-Dong Chen, Xiao-Rong Yang, Xue-Meng Shang

“…Lack of CD8+ TRM might be a key factor responsible for the suppressive TME of EGFR-mutant LUAD.…”
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Elucidating the dynamic tumor microenvironment through deep transcriptomic analysis and therapeutic implication of MRE11 expression patterns in hepatocellular carcinoma by Ruiqiu Chen, Chaohui Xiao, Zizheng Wang, Guineng Zeng, Shaoming Song, Gong Zhang, Lin Zhu, Penghui Yang, Rong Liu

“…Publicly available single-cell RNA sequencing (scRNA-seq) data and spatial transcriptomics were utilized to explore MRE11’s dynamic mechanisms in the tumor microenvironment (TME) of both primary and post-immunotherapy cases. …”
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Multi-region brain transcriptomic analysis of amyotrophic lateral sclerosis reveals widespread RNA alterations and substantial cerebellum involvement by Natalie Grima, Andrew N. Smith, Claire E. Shepherd, Lyndal Henden, Thiri Zaw, Luke Carroll, Dominic B. Rowe, Matthew C. Kiernan, Ian P. Blair, Kelly L. Williams

“…Methods We generated 165 sample-matched post-mortem brain transcriptomes from 22 sporadic ALS patients with pTDP-43 pathological staging and 11 non-neurological controls. …”
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Integrated Transcriptomic and Proteomic Analyses Reveal CsrA-Mediated Regulation of Virulence and Metabolism in <i>Vibrio alginolyticus</i> by Bing Liu, Huizhen Chen, Kai Sheng, Jianxiang Fang, Ying Zhang, Chang Chen

“…Increasing evidence suggests that post-transcriptional regulation by RNA-binding proteins and small RNAs (sRNAs) plays a crucial role in bacterial adaptation and metabolism. …”
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