Trans-ancestry transcriptome-wide association and functional studies to uncover novel susceptibility genes and therapeutic targets for colorectal cancer by Lijuan Wang, Lidan Hu, Jing Sun, Jianhui Zhao, Siyun Zhou, Lexin Liu, Wei Yu, Yeting Hu, Dan Zhou, Xiangrui Meng, Zhongshang Yuan, Honghe Zhang, Susan Farrington, Maria Timofeeva, Kefeng Ding, Julian Little, Malcolm Dunlop, Evropi Theodoratou, Xue Li

“…We first conducted a trans-ancestry transcriptome-wide association study (TWAS) among 57,402 CRC cases and 119,110 controls, aiming to examine how altered gene expression influences CRC risk in European and Asian populations. …”
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Comparative transcriptomics reveal contrasting strategies between a fungal plant pathogen and an endophyte during initial host colonization by Soumya Moonjely, Frances Trail

“…However, their contrasting roles as pathogen and endophyte provide an excellent model for exploring initial colony establishment on the hosts. …”
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Global Transcriptome Analysis Reveals Distinct Aluminum-Tolerance Pathways in the Al-Accumulating Species Hydrangea macrophylla and Marker Identification. by Haixia Chen, Changping Lu, Hui Jiang, Jinhui Peng

“…The assembly of hydrangea transcriptome provides a rich source for gene identification and mining molecular markers, including single nucleotide polymorphism (SNP) and simple sequence repeat (SSR). …”
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Genomic, transcriptomic, and T cell receptor profiling in stratifying response to first-line chemoradiotherapy or radiotherapy for esophageal squamous cell carcinoma by Xiaqin Zhang, Jianhong Lian, Fukun Chen, Kai Wang, Haoyuan Xue, Sufang Jia, Weili Wang, Zhongkang Li, Hua Liang, Hongwei Li

“…The molecular characteristics of locally advanced ESCC have been extensively studied.MethodsIn this study, we investigate the genomic and transcriptomic characteristics and try to provide the basic T-cell receptors (TCRs) dynamics and its genomic and transcriptome association during the radiochemotherapy of ESCC using multi-omics analysis.ResultsA total of 23 patients with pathologic diagnoses of locally advanced ESCC were enrolled. …”
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The Characteristics and Functions of SSRs and SNPs Based on the Transcriptome of <i>Tuta absoluta</i> Exposed to Different Concentrations of Abamectin and Chlorantraniliprole by Fanxue Zhang, Meimei Mu, Zonglin Wang, Haoran Zhang, Yilan Song, Rong Xiao

“…In this study, based on the previously obtained transcriptome data, a total of 25,123 SSR loci and 332,537 SNP loci were identified. …”
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Time-course transcriptome analysis reveals gene co-expression networks and transposable element responses to cold stress in cotton by Yan Dai, Jialiang Zhou, Baohong Zhang, Dewei Zheng, Kai Wang, Jinlei Han

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Dynamic transcriptomics unveils parallel transcriptional regulation in artemisinin and phenylpropanoid biosynthesis pathways under cold stress in  Artemisia annua by Yunxiao He, Wenjing Zhang, Xianghua Zuo, Jiangnan Li, Ming Xing, Yujiao Zhang, Jian You, Wei Zhao, Xia Chen

“…The accumulation of total organic carbon (TOC) in leaves under cold stress provided ample precursors for secondary metabolite synthesis. …”
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Accurate Transcription Factor Activity Inference to Decipher Cell Identity from Single‐Cell Transcriptomic Data with MetaTF by Yongfei Hu, Yuanyuan Zhu, Guangjue Tang, Ming Shan, Puwen Tan, Ying Yi, Xiyuan Zhang, Man Liu, Xinyu Li, Le Wu, Jia Chen, Hailong Zheng, Yan Huang, Zhuan Li, Xiaobo Li, Dong Wang

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Sea lice (Lepeophtheirus salmonis) life stage impacts atlantic salmon transcriptomic responses under different thermal profiles by Reza Ghanei-Motlagh, Reza Ghanei-Motlagh, Wenlong Cai, Jordan D. Poley, Shona K. Whyte, Amber F. Garber, Mark D. Fast

“…Given the complexity of host-parasite interactions, family-based transcriptomic studies provide crucial insights into genetic variation in host responses to sea lice, potentially guiding the development of selective breeding programs to manage parasite resistance in Atlantic salmon. …”
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Single-cell and spatial transcriptomics analysis reveals that Pros1+ oligodendrocytes are involved in endogenous neuroprotection after brainstem stroke by Shaojun Li, Guanfeng Zeng, Chunmei Pang, Jie Li, Li Wu, Ming Luo, Zhihua Qiu, Yongjun Jiang

“…As the predominant cellular component of nerve tracts, oligodendrocytes might provide some neuroprotection against ischemic injury in the context of brainstem stroke, but the underlying mechanism remains unclear. …”
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Metabolomic and Transcriptomic Insights into Quality Formation of Orange-Red Carrot (<i>Daucus carota</i> L.) During Maturation by Chongzhen Gao, Hongtao Zhang, Jiayu Wang, Ziqing Guo, Ruixue Shen, Weilong Zhu, Tianyue Song, Hongxia Song

“…Studying metabolic changes during carrot maturation can provide deeper insights into the formation of their nutritional value and quality. …”
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Integrated Transcriptomic and Metabolomic Analyses Reveal the Importance of the Terpenoid, Fatty Acid, and Flavonoid Pathways in Rice Cell Death and Defense by Pengfei Bai, Yanfang Liu, Laisa Gomes-Dias, Rachel Combs-Giroir, Shaoxing Dai, Naeyeoung Choi, Yun Lin, Matthew Bernier, Emmanuel Hatzakis, Guo-Liang Wang, Joshua J. Blakeslee

“…These changes are likely correlated with the observed cell death and resistance phenotypes in the SDS2-ACT mutant. This study provides an overall landscape of the transcriptomic and metabolomic alterations in a lesion mimic mutant, identifying candidate defense-related genes and metabolites for functional analysis in rice.…”
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Unveiling the molecular mechanism of sepal curvature in Dendrobium Section Spatulata through full-length transcriptome and RNA-seq analysis by Xuefeng Qu, Na Li, Cong Xu, Zifeng Huang, Chunyan Li, Yang Jiang, Guizhao Zheng, Haiping Fu, Guangyan Zhang, Chuan Liu

“…Cytological microscopy was used to examine cell size and number, and quantitative real-time PCR (qRT-PCR) was performed to validate transcriptomic findings.ResultsThe reference transcriptome contained 94,258 non-redundant transcripts, and RNA-seq identified 821 DEGs between sepals and petals, with 72.8% of these upregulated in sepals. …”
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Transcriptome remodeling drives acclimation to iron availability in the marine N2-fixing cyanobacterium Trichodesmium erythraeum IMS101 by Xin Zhong, Ran Duan, Shengwei Hou, Meng Chen, Xiaoming Tan, Wolfgang R. Hess, Tuo Shi

“…Here, we show in a laboratory setup mimicking Fe fertilization in the field that transcriptome remodeling is a primary driver of acclimation to Fe availability in the marine diazotrophic cyanobacterium Trichodesmium erythraeum IMS101. …”
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Transcriptomic Profiling Uncovers Molecular Basis for Sugar and Acid Metabolism in Two Pomegranate (<i>Punica granatum</i>) Varieties by Ding Ke, Yilong Zhang, Yingfen Teng, Xueqing Zhao

“…Soluble sugars and organic acids constitute the primary flavor determinants in fruits and elucidating their metabolic mechanisms provides crucial theoretical foundations for fruit breeding practices and food industry development. …”
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Integrative Transcriptomic and Metabolomic Analysis Reveals the Molecular Mechanisms Underlying Flowering Time Variation in <i>Camellia</i> Species by Ling Zhou, Tao Guo, Shihui Zou, Lingli Li, Xuemei Li, Jiao Wang, Zilin Zhu, Lijiao Ai

“…Although the discovery of <i>Camellia azalea</i> provides important germplasm resources for developing cultivars with year-round flowering, the molecular mechanisms underlying flowering time variation remain unclear. …”
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New genomic resources inform transcriptomic responses to heavy metal toxins in the common Eastern bumble bee Bombus impatiens by Amy L. Toth, Christopher D. R. Wyatt, Rick E. Masonbrink, Katherine S. Geist, Ryan Fortune, Sarah B. Scott, Emeline Favreau, Sandra M. Rehan, Seirian Sumner, Mary M. Gardiner, Frances S. Sivakoff

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The key metabolic genes and networks regulating the fruit acidity and flavonoid of Prunus mume revealed via transcriptomic and metabolomic analyses by Xuan Gao, Shuangshuang Wu, Guosheng Lv, Mengyang Wang, Lingxiang Li, Yahui Liu, Feng He, Jiaxin Xiao

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Early transcriptomic changes in cucumber and maize roots in response to FePO4 nanoparticles as a source of P and Fe by Andrea Ciurli, Anita Zamboni, Zeno Varanini

“…This supposition is confirmed by transcriptomic profiles that show no significant upregulation of transcripts typically induced by deficiencies in P and Fe in cucumber and maize plants in which these nutrients were provided by FePO4 nanoparticles. …”
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PoweREST: Statistical power estimation for spatial transcriptomics experiments to detect differentially expressed genes between two conditions. by Lan Shui, Anirban Maitra, Ying Yuan, Ken Lau, Harsimran Kaur, Liang Li, Ziyi Li, Translational and Basic Science Research in Early Lesions Research Consortia

“…Recent advancements in spatial transcriptomics (ST) have significantly enhanced biological research in various domains. …”
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