Combining metabolomic and transcriptomic approaches to assess and improve crop quality traits by Delphine M. Pott, Sara Durán-Soria, Sonia Osorio, José G. Vallarino

“…Recent technical advances in high throughput metabolomic, transcriptomic and genomic platforms have provided efficient approaches to identify new genes and pathways responsible for the extremely diverse plant metabolome. …”
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Multidimensional Transcriptomics Reveals the Key Genes and Pathways Regulating the Acidity of Apples by Wenyuan Yang, Hang Yu, Lian Tao, Hongjiang Xie

“…In both apples, quinic and malic acids were the predominant organic acids, while citric and tartaric acids were present in lower amounts. …”
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Transcriptome analysis of Ipomoea cairica algicidal mechanism against Phaeocystis globosa by Dayong Liang, Huanxin Li, Yuxuan Pan, Zihan Liu, Hua Xiang

“…In this study, control groups were treated with sterile seawater, while experimental groups were exposed to I. cairica extracts (final concentration of 1%). …”
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STsisal: a reference-free deconvolution pipeline for spatial transcriptomics data by Yinghao Fu, Yinghao Fu, Yinghao Fu, Leqi Tian, Weiwei Zhang

“…Spatial transcriptomics has emerged as an invaluable tool, helping to reveal molecular status within complex tissues. …”
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Transcriptomic and functional analysis of triphenyl phosphate exposure in prostate cancer progression by Li Cai, Guizhi Du

“…Methods We conducted transcriptomic profiling using mRNA sequencing to investigate gene expression changes in prostate cancer cells following TPP exposure. …”
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Functional and transcriptomic insights into plant response to arginine-functionalized nanohydroxyapatite treatment by Chinenye L. Izuegbunam, Beate Wone, Bernard W.M. Wone

“…Despite the potential advantages of nHA-mediated biomolecule delivery and its application as fertilizers, phytotoxicity concerns necessitate additional studies. While initial findings suggest the beneficial effects of nHA as a nanofertilizer at specific concentrations, a thorough investigation into its bioactivity is warranted. …”
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The DNA methylome and transcriptome of different brain regions in schizophrenia and bipolar disorder. by Yun Xiao, Cynthia Camarillo, Yanyan Ping, Tania Bedard Arana, Hongying Zhao, Peter M Thompson, Chaohan Xu, Bin Brenda Su, Huihui Fan, Javier Ordonez, Li Wang, Chunxiang Mao, Yunpeng Zhang, Dianne Cruz, Michael A Escamilla, Xia Li, Chun Xu

“…Furthermore, DMRs in the same brain regions from SC and BP could successfully distinguish BP and/or SC from normal controls while differentially expressed genes could not. Overall, our results support a major role for brain-region-dependent aberrant DNA methylation in the pathogenesis of these two disorders.…”
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Physiological and transcriptomic analysis of Spartina alterniflora in response to imazapyr acid stress by Yaning Liu, Zhengmao Li, Lixia Li, Xiangyang Jiang, Chen Gao, Jiqiang Zhao

“…In this study, we applied 6.0 L/acre of 25% imazapyr acid aqueous stress treatment, and determined and analyzed the physiological activities and transcriptome profiles of S. alterniflora under sustained stress. …”
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Gene fusion detection in long-read transcriptome sequencing data with GFvoter by Xiaolan Zhao, Zitong Ren, Junhai Qi, Enfeng Qi, Xiaoyu Zhao, Guojun Li, Ting Yu

“…Moreover, GFvoter successfully reported the RPS6KB1:VMP1 gene fusion in the MCF-7 cell line, while none of the other tested tools detected this fusion. …”
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Integrated analysis of intestinal microbial community and muscle transcriptome profile in rabbits by Shengbo Meng, Shanshan Xing, Huifen Xu, Jing Li, Yixuan Jiang, Hui He, Hanfang Cai, Ming Li

“…In order to better understand the relationship between gut microbiota and gene expression in skeletal muscle of rabbits, caecum contents and longissimus dorsi tissues of rabbits at 0 d (S1), 35 d (S2) and 70d (S3) were collected and subjected for 16S rRNA sequencing and transcriptome sequencing. Our results showed that, among three groups of rabbits, Firmicutes and Bacteroidetes were the dominant phyla at the phylum level, while Akmansia, Bacteroides and Ruminobacter were the dominant genera at the genus level, and the relative abundance of Akmansia and Bacteroides increased firstly and then decreased from 0 d to 70 d. …”
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Codes between Poles: Linking Transcriptomic Insights into the Neurobiology of Bipolar Disorder by Jon Patrick T. Garcia, Lemmuel L. Tayo

“…The nAcc was found to be highly associated with genes responsible for the deregulated transcription of neurotransmitters, while the DLPFC was greatly correlated with genes involved in the impairment of components crucial in neurotransmission. …”
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Transcriptomic Profile of Tef (<i>Eragrostis tef</i>) in Response to Drought by Lorena Ramirez-Gonzales, Gina Cannarozzi, Abiel Rindisbacher, Lea Jäggi, Regula Schneider, Annett Weichert, Sonia Plaza-Wüthrich, Solomon Chanyalew, Kebebew Assefa, Zerihun Tadele

“…Trotter] is an allotetraploid cereal crop that is a staple food for a large population in the Horn of Africa. While the grain of tef provides quality food for humans, its straw is the most palatable and nutritious feed for livestock. …”
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Transcriptomic and epigenetic responses shed light on soybean resistance to Phytophthora sansomeana by Gwonjin Lee, Charlotte N. DiBiase, Beibei Liu, Tong Li, Austin G. McCoy, Martin I. Chilvers, Lianjun Sun, Dechun Wang, Feng Lin, Meixia Zhao

“…Abstract Phytophthora root rot, caused by oomycete pathogens in the Phytophthora genus, poses a significant threat to soybean productivity. While resistance mechanisms against Phytophthora sojae have been extensively studied in soybean, the molecular basis underlying immune responses to Phytophthora sansomeana remains unclear. …”
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The interplay between epigenomic and transcriptomic variation during ecotype divergence in stickleback by Man Luo, Junjie Zhao, Juha Merilä, Rowan D. H. Barrett, Baocheng Guo, Juntao Hu

“…Abstract Background Populations colonizing contrasting environments are likely to undergo adaptive divergence and evolve ecotypes with locally adapted phenotypes. While diverse molecular mechanisms underlying ecotype divergence have been identified, less is known about their interplay and degree of divergence. …”
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Transcriptomic Response of White Lupin Roots to Short-Term Sucrose Treatment by Proyasha Roy, Shrey Sethi, James New, Kristina Mae Lorilla, Karen Maleski, Allan Ancheta, Claudia Uhde-Stone

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Transcriptomic and metabolomic insights into flavor variations in wild and cultivated Agaricus bisporus by Zhi-Xin Cai, Zhi-Heng Zeng, Wen-Zhi Chen, Zhong-Jie Guo, Yuan-Ping Lu, Jian-Hua Liao, Hui Zeng, Mei-Yuan Chen

“…Metabolomic analysis further revealed a marked increase in uridine levels in cultivated strains (3.2-fold higher than wild-type, p < 0.01), indicating potential medicinal value, while wild strains were enriched with flavor precursors such as fumaric acid and isoleucine (fold change ≥ 2.5). …”
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Transcriptomic analysis of the symbiotic responsivity trait in pea (Pisum sativum L.) by D. O. Kuzmina, E. A. Zorin, A. S. Sulima, D. A. Romanyuk, M. L. Gordon, A. I. Zhernako, O. A. Kulaeva, G. A. Akhtemova, O. . Shtark, I. A. Tikhonovich, V. A. Zhukov

“…Further work will be focused on validation of these transcriptomic markers of the symbiotic responsivity trait in pea.…”
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Polygenic transcriptome risk scores enhance predictive accuracy in atopic dermatitis by Charalabos Antonatos, Ashley Budu-Aggrey, Alexandros Pontikas, Adam Akritidis, Efstathia Pasmatzi, Aikaterini Tsiogka, Stamatis Gregoriou, Katerina Grafanaki, Lavinia Paternoster, Yiannis Vasilopoulos

“…Methods We conducted transcriptome-wide association studies (TWAS) using the PrediXcan framework to construct tissue-specific PTRSs. …”
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Transcriptome sequencing of Antheraea pernyi antennae for identification of olfactory-related genes by Xueting Liu, Shuwei Ma, Xinxue Zhang, Xue Li, Lei Nie, Guobao Wang

“…Hence, we aimed to conduct transcriptome sequencing to explore olfactory-related genes in the antennae, serving as the most important olfactory organ in adult A. pernyi. …”
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Transcriptome analysis of sugar beet in response to the pathogenic oomycete Aphanomyces cochlioides by Valentina Rossi, Louise Holmquist, Erik Alexandersson, Laura Grenville-Briggs

“…With the aim to identify key genes involved in plant defense responses against the root rot, we performed a transcriptome analysis of sugar beet interactions with A. cochlioides. …”
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