De Novo Assembly and Comparative Transcriptome Analysis Provide Insight into Lysine Biosynthesis in Toona sinensis Roem by Xia Zhang, Zhenqiao Song, Tian Liu, Linlin Guo, Xingfeng Li

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The Role of Genomics and Transcriptomics in Characterizing and Predicting Patient Response to Treatment in Triple Negative Breast Cancer (TNBC) by Franklin Eduardo Corea-Dilbert, Muhammad Zubair Afzal

“…These unique elements are the foundation of personalized medicine where genomics and transcriptomics play a critical role in increasing granularity in patients’ disease and treatment. …”
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Anatomy and transcriptomics of the common jingle shell (Bivalvia, Anomiidae) support a sensory function for bivalve tentacles by Jorge A. Audino, Kyle E. McElroy, Jeanne M. Serb, José E. A. R. Marian

“…In addition to applying microscopy techniques, we performed transcriptome sequencing of dissected tentacles using phylogenetically-informed annotation to identify candidate receptors. …”
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Single-cell transcriptomic landscape reveals complex cellular heterogeneity and dysregulated signaling pathways in nasopharyngeal carcinoma by Xiaoyan Zhang, Zuojia Guan, Zhan Xu

“…This study aimed to systematically analyze the transcriptional characteristics of different cell types in NPC and their roles in tumor development using single-cell transcriptomics. …”
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Transcriptomic characterization of maturing neurons from human neural stem cells across developmental time points by Kimia Hosseini, Gaëtan Philippot, Sara B. Salomonsson, Andrea Cediel-Ulloa, Elnaz Gholizadeh, Robert Fredriksson

“…Ion AmpliSeq™ was used for transcriptomic characterization of human stem cell-derived neurons at multiple time points. …”
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De novo assembly of the common bean transcriptome using short reads for the discovery of drought-responsive genes. by Jing Wu, Lanfen Wang, Long Li, Shumin Wang

“…The strategy for de novo assembly of transcriptome data generated here will be useful in other legume plant transcriptome studies. …”
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Combined transcriptome and proteome profiling reveal cell-type-specific functions of Drosophila garland and pericardial nephrocytes by Heiko Meyer, Judith Bossen, Maren Janz, Xenia Müller, Sven Künzel, Thomas Roeder, Achim Paululat

“…Here, we established a method for cell-specific isolation of the two types of Drosophila nephrocytes, garland and pericardial cells, from animals of different developmental stages and ages. Mass spectrometry-based proteomics and RNA-Seq-based transcriptomics were applied to characterise the proteome and transcriptome of the respective cells in an integrated and complementary manner. …”
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Comparative Transcriptome Analysis of Hens’ Livers in Conventional Cage vs. Cage-Free Egg Production Systems by María Paula Herrera-Sánchez, Roy Rodríguez-Hernández, Iang Schroniltgen Rondón-Barragán

“…Different conditions of production systems including stocking density, thermal conditions, and behavior restriction can have a significant detrimental effect on the health and performance of laying hens. …”
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Integration of Single-Cell and Bulk Transcriptome to Reveal an Endothelial Transition Signature Predicting Bladder Cancer Prognosis by Jinyu Yang, Wangxi Wu, Xiaoli Tang

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MENGA: A New Comprehensive Tool for the Integration of Neuroimaging Data and the Allen Human Brain Transcriptome Atlas. by Gaia Rizzo, Mattia Veronese, Paul Expert, Federico E Turkheimer, Alessandra Bertoldo

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From the environment to the host: re-wiring of the transcriptome of Pseudomonas aeruginosa from 22°C to 37°C. by Mariette Barbier, F Heath Damron, Piotr Bielecki, María Suárez-Diez, Jacek Puchałka, Sebastian Albertí, Vitor Martins Dos Santos, Joanna B Goldberg

“…We examined the effects of growth temperature on the transcriptome of the P. aeruginosa PAO1. Microarray analysis of PAO1 grown in Lysogeny broth at mid-exponential phase at 22°C and 37°C revealed that temperature changes are responsible for the differential transcriptional regulation of 6.4% of the genome. …”
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Spatial transcriptomics identifies RBM39 as a gene associated with Gleason score progression in prostate cancer by Yongjun Quan, Mingdong Wang, Hong Zhang, Dan Lu, Hao Ping

“…Principal component analysis (PCA) and Louvain clustering analysis revealed transcriptomic classifications aligned with the histology of different GSs. …”
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NGS Transcriptomes and Enzyme Inhibitors Unravel Complexity of Picrosides Biosynthesis in Picrorhiza kurroa Royle ex. Benth. by Kirti Shitiz, Neha Sharma, Tarun Pal, Hemant Sood, Rajinder S Chauhan

“…Retrieval of gene sequences for enzymatic steps from NGS transcriptomes and their expression analysis vis-à-vis picrosides content in different tissues/organs showed elevated transcripts for twenty genes, which were further shortlisted to seven key genes, ISPD, DXPS, ISPE, PMK, 2HFD, EPSPS and SK, on the basis of expression analysis between high versus low picrosides content strains of P. kurroa so as to eliminate tissue type/ developmental variations in picrosides contents. …”
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Transcriptome-aligned metabolic profiling by SERSome reflects biological changes following mesenchymal stem cells expansion by Xinyuan Bi, Bin Ma, Wei Liu, Wei-Qiang Gao, Jian Ye, Hanyu Rao

“…By integrating these metabolic features detected by SERS with transcriptomic data, we established a correlation between SERS signals and biological changes, as well as differentially expressed genes. …”
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Comparative transcriptomic analysis of chicken immune organs affected by Marek’s disease virus infection at latency phases by Yi Ding, John Dunn, Huanmin Zhang, Keji Zhao, Jiuzhou Song

“…We identified genes and pathways associated with the transcriptional response to MDV infection using the robust RNA sequencing approach. The transcriptome analysis revealed a tissue-specific expression pattern among immune organs when confronting MDV. …”
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Deciphering the dose-dependent effects of thymoquinone on cellular proliferation and transcriptomic changes in A172 glioblastoma cells. by Rachana Pandey, Purushothaman Natarajan, Umesh K Reddy, Wei Du, Cristian Sirbu, Moussa Sissoko, Gerald R Hankins

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Integrated morphological observation, metabolomics, and transcriptomics to investigate the effect of growth years on the quality of Atractylodes macrocephala Koidz by Xiaoxuan Cui, Yihan Wang, Guoliang Yu, Bowei He, Luqi Huang, Yanmeng Liu, Zhilai Zhan

“…However, research on its quality dynamics across different growth years remains limited, primarily focusing on transcriptomics, microbiome analysis, and photosynthetic capacity, with studies only extending to three-year-old plants. …”
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Integrated transcriptomic and metabolomic analysis of flavonoid biosynthesis in cigar tobacco leaves under variable nitrogen regimes by Kai Jia, Juanjuan Shi, Lingli Bai, Xueren Wang, Yuemin Wang, Xiangzhen Li, Wenqing Li, Chaoyuan Zheng

“…Given tobacco's high nitrogen demand and the particular sensitivity of flavonoid synthesis to nitrogen supply, understanding the regulatory mechanisms of flavonoid biosynthesis under varying nitrogen conditions is essential.Methods and resultsWe systematically investigated the flavonoid biosynthesis pathways in the cigar tobacco cultivar Haiyan 204 under different nitrogen application rates using integrated transcriptomic and metabolomic analyses. …”
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Transcriptomic Analysis Reveals the Mechanisms of Cadmium Transport and Detoxification in Portuguese Oysters (<i>Crassostrea angulata</i>) by Kairui Qin, Longping Wu, Shixing Fu, Huayong Que, Bo Shi

“…Individuals with significantly different Cd accumulation were selected for transcriptomic sequencing analysis. …”
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Transcriptomic and proteomic analysis of oil body associated protein dynamics in the biofuel feedstock Pennycress (Thlaspi arvense) by María Ángeles Luján, Ana Claver, Patricia Lorente, M. Victoria López, Miguel Alfonso

“…A combination of transcriptomic and proteomic tools was used to characterize the dynamics and relative abundance of the major oil body related proteins in the Pennycress seed. …”
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