A benchmark of RNA-seq data normalization methods for transcriptome mapping on human genome-scale metabolic networks by Hatice Büşra Lüleci, Dilara Uzuner, Müberra Fatma Cesur, Atılay İlgün, Elif Düz, Ecehan Abdik, Regan Odongo, Tunahan Çakır

“…In this study, we aimed to compare five different RNA-seq data normalization methods (TPM, FPKM, TMM, GeTMM, and RLE) and covariate adjusted versions of the normalized data by mapping them on a human GEM using the iMAT and INIT algorithms to generate personalized metabolic models. …”
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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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Identification of crucial drought-tolerant genes of barley through comparative transcriptomic analysis and yeast-based stress assay by Xiaoyan He, Congjun Su, Xinyi Zhang, Zhaoxia Shi, Yanjie Wang, Huandi Peng, Shuying Fang, Xinyu Chen, Huayan Yin, Jianbin Zeng, Ping Mu

“…Transcriptomic sequencing data from the aboveground parts of these plants led to the identification of 1,206 differentially expressed genes associated with drought tolerance. …”
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Transcriptome dataset to investigate the effect of deep seawater on the gene expression and functional compounds of leaves of Ligularia stenocephalaNCBI. by Dewi Komang Anggita, Bimpe Suliyat Azeez, Se-Jin Oh, Jong-Kuk Na

“…Due to the lack of the reference genome for read mapping, the three transcriptome data from this study were merged to generate a reference transcriptome. …”
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Insights into the Antimicrobial Mechanisms of a Scorpion Defensin on <i>Staphylococcus aureus</i> Using Transcriptomic and Proteomic Analyses by Xuhua Yang, Haozhen Zhang, Sijia Lu, Yiyuan Guo, Yitong Li, Chenhu Qin, Zheng Zuo, Yingliang Wu, Zhijian Cao

“…Defensins constitute a family of cationic antimicrobial peptides that act against different bacteria; however, global information regarding their antibacterial mechanisms from omics-based analyses is highly limited. …”
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Differential Gene Expression during Larval Metamorphic Development in the Pearl Oyster, Pinctada fucata, Based on Transcriptome Analysis by Haimei Li, Bo Zhang, Guiju Huang, Baosuo Liu, Sigang Fan, Dongling Zhang, Dahui Yu

“…Expression profiles were distinctly different between trochophore, D-shape, umbonal, eyespots, and spats larvae. …”
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Root Ethylene and Abscisic Acid Responses to Flooding Stress in <i>Styrax japonicus</i>: A Transcriptomic Perspective by Chao Han, Jinghan Dong, Gaoyuan Zhang, Qinglin Zhu, Fangyuan Yu

“…Two levels of flooding stress, waterlogging and submergence, were applied to examine the variations in endogenous hormone levels in <i>S. japonicus</i> roots under different stress conditions and durations. Combined with transcriptome sequencing, critical genes associated with hormone-mediated signaling and biosynthetic processes were identified. …”
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Genome, transcriptome and secretome analyses of the antagonistic, yeast-like fungus Aureobasidium pullulans to identify potential biocontrol genes by Maria Paula Rueda-Mejia, Lukas Nägeli, Stefanie Lutz, Richard D. Hayes, Adithi R. Varadarajan, Igor V. Grigoriev, Christian H. Ahrens, Florian M. Freimoser

“…Aureobasidium pullulans is an extremotolerant, cosmopolitan yeast-like fungus that successfully colonises vastly different ecological niches. The species is widely used in biotechnology and successfully applied as a commercial biocontrol agent against postharvest diseases and fireblight. …”
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Metabolomics and transcriptomics analyses reveal the complex molecular mechanisms by which the hypothalamus regulates sexual development in female goats by Qing Li, Tianle Chao, Yanyan Wang, Peipei He, Lu Zhang, Jianmin Wang

“…In this study, we conducted metabolomic and transcriptomic analyses on the hypothalamic tissues of female Jining grey goats at different stages of sexual development (1 day old (neonatal, D1, n = 5), 2 months old (prepuberty, M2, n = 5), 4 months old (sexual maturity, M4, n = 5), and 6 months old (breeding period, M6, n = 5)). …”
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Transcriptomic and physiological insights into auxin-mediated root growth and potassium uptake in tobacco under low-potassium stress by Kunhao Guan, Yingying Li, Yuyin Zhang, Jie Yang, Zixuan Ge, Xiaoyan Dai

“…Under these conditions, exogenous Indole acetic acid (IAA) enhanced root development and increased potassium uptake, whereas N-1-naphthylphthalamic acid (NPA) inhibited root growth and adversely affected potassium absorption and retention. Transcriptome sequencing under low-potassium conditions identified 8,381 differentially expressed genes (DEGs) between the two different treatment groups that were primarily enriched in pathways related to photosynthesis-antenna proteins, photosynthesis, plant hormone signal transduction, and the MAPK signaling pathway. …”
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Integrated metabolome and transcriptome analysis provides clues to fruit color formation of yellow, orange, and red bell pepper by Qiqin Xue, Qingxia Zhang, Aiai Zhang, Da Li, Yongguang Liu, Haicheng Xu, Qinghua Yang, Fengyan Liu, Tongyao Han, Xiaozhen Tang, Xiurong Zhang

“…To investigate the mechanism of color formation, three bell pepper lines with different color (yellow, orange and red) were used as materials to conduct comprehensive targeted metabolomic and transcriptomic analyses. …”
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Transcriptome reveals the roles and potential mechanisms of CeRNA in the regulation of salivary gland development in the tick Rhipicephalus haemaphysaloides by Shanming Hu, Songqin Chen, Haotian Zhu, Yanan Wang, Yongzhi Zhou, Jie Cao, Houshuang Zhang, Jinlin Zhou

“…However, the comprehensive expression profile and competing endogenous RNA (ceRNA) regulatory network between mRNAs and ncRNAs involved in salivary gland development remain unclear.MethodsIn the current study, we employed whole-transcriptome sequencing (RNA sequencing) at various stages of feeding to identify differentially expressed lncRNAs, circRNAs, miRNAs, and mRNAs. …”
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Comprehensive Profiling of Transcriptome and m6A Epitranscriptome Uncovers the Neurotoxic Effects of Yunaconitine on HT22 Cells by Beian Lin, Jian Zhang, Mengting Chen, Xinyue Gao, Jiaxin Wen, Kun Tian, Yajiao Wu, Zekai Chen, Qiaomei Yang, An Zhu, Chunhong Du

“…Objective: To explore different mRNA transcriptome patterns and RNA N6-methyladenosine (m6A) alteration in yunaconitine (YA)-treated HT22 mouse hippocampal neuron, and uncover the role of abnormal mRNA expression and RNA m6A modification in YA-induced neurotoxicity. …”
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Transcriptomic and Metabolomic Characterization of Volatile Flavor Compound Dynamics in Dragon Fruit (<i>Selenicereus</i> spp.) Development by Zhi-Jiang Wu, Ri-Wen Ji, Ze-Jian Huang, Xiao-Ying Ye, Li-Fang Huang, Hai-Yan Deng, Gui-Feng Lu, Shuo-Tong Wei, Chao-An Liu, Zhen-Ying Li, Hong-Li Li, Gui-Dong Liang

“…To this end, we sequenced the transcriptomes and metabolomes of red-skin/white-fleshed and red-skin/red-fleshed dragon fruit at different timepoints during fruit development. …”
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Integrated Transcriptomic and Metabolomic Provide Insights into Strawberry Bioactive Compounds and Antioxidant Activities Under Varying Ecological Conditions by Mingzheng Duan, Huaizheng Wang, Kangjian Song, Honggao Liu, Shu Jiang, Jieming Feng, Shiping Jiang, Muhammad Junaid Rao, Abdul Rauf, Muhammad Ikram, Muhammad Faizan Khurram, Maryam Tahira, Shunqiang Yang, Xiande Duan

“…In this study, a transcriptomic and LC–MS/MS approach identified several biosynthesis genes, 33 alkaloids, and 38 other bioactive compounds, reported for the first time in the strawberry fruits. …”
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Single-cell transcriptome sequencing reveals the immune microenvironment in bronchoalveolar lavage fluid of checkpoint inhibitor-related pneumonitis by Linpeng Zheng, Fenglin Lin, Dingqin Cai, Longyao Zhang, Chenrui Yin, Yaxian Qi, Lingyou Sun, Lingchen Li, Xiewan Chen, Jianbo Zhu, Jianguo Sun

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Spatial transcriptomic characteristics of gastric cancer in young and the expression and role of TMEM176B in gastric cancer cells by Zhenhua Jiang, Yongfeng Wang, Chi Zhang, Shuangyin Han

“…Conclusions This study used ST-seq to map the transcriptomic profiles of the TCR, CAT, and NGT in patients with GCY, investigating gene spatial expression patterns and tumor heterogeneity. …”
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Comparative transcriptome analysis on candidate genes involved in lipid biosynthesis of developing kernels for three walnut cultivars in Xinjiang by Wenqiang Wang, Hao Wen, Qiang Jin, Wenjun Yu, Gen Li, Minyu Wu, Hongjin Bai, Lirong Shen, Cuiyun Wu

“…In order to explore the biosynthesis molecular mechanism of oil accumulation and fatty acid (FA) synthesis in walnut, the samples at different development periods of three walnut cultivars, ‘Zhipi’ (ZP), ‘Xinwu 417’ (W417) and ‘Xinwen 81’ (W81) were collected for transcriptomic analysis. …”
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Splenic comparative transcriptome analysis reveals the immunological mode of undomesticated Gayal (Bos frontalis) for adapting to harsh environments by Ye Yu, Chunjia Jin, Runqi Fu, Lin Han, Binlong Fu, Qian Li, Yanfen Cheng, Jing Leng

“…However, research on immune function of gayal is limited, and comparisons with different breeds are rarely reported. The objective of this study was to inspect the immune status and compare splenic differential expression genes (DEGs) through comparative transcriptome analysis of gayal and domesticated local cattle (Yunan yellow cattle). …”
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De Novo Leaf Transcriptome Assembly and Metagenomic Studies of Coast Live Oak (<i>Quercus agrifolia</i>) by Savanah Senn, Ray A. Enke, Steven J. Carrell, Bradley Nations, Meika Best, Mathew Kostoglou, Karu Smith, Jieyao Yan, Jillian M. Ford, Les Vion, Gerald Presley

“…There was a differential abundance of microbial genera associated with the different burn areas, including <i>Pedobacter</i>, <i>Filimonas</i>, <i>Cohnella</i>, and <i>Sorangium</i>. …”
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