Transcriptome and Anthocyanin Profile Analysis Reveals That Exogenous Ethylene Regulates Anthocyanin Biosynthesis in Grape Berries by Min Liu, Boyuan Fan, Le Li, Jinmei Hao, Ruteng Wei, Hua Luo, Fei Shi, Zhiyuan Ren, Jun Wang

“…In EHT-treated berries, 19 MYB and 23 ERF genes were expressed differently compared with the control (<i>p</i> < 0.05). …”
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Heat stress induces specific methylation, transcriptomic and metabolic pattern in dairy cows and their female progeny by Kathrin Halli, Tong Yin, Christian Koch, Stefan Krebs, Sven König

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Transcriptomic and targeted metabolomic analysis identifies genes involved in differential anthocyanin accumulation in potato tubers by Rui Yang, Shuohan Huang, Dan Li, Yuan Sun, Guangdong Zhou, Duanrong Zhou, Binquan Huang

“…To identify genes and metabolites involved in anthocyanin accumulation, we performed comparative transcriptomic and metabolomic analyses of pith and vasculature tissues from the tubers of three different potato cultivars. …”
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Transcriptome reveal gene regulation mechanisms of the barnacle Chthamalus challengeri for microhabitat adaption in the intertidal zone by HaoYuan Li, MengMeng Huang, ZhiBin Gan, XinZheng Li

“…Results In this study, we designed a series of in situ tidal conditions for C. challengeri and sequenced their transcriptome collected from various microhabitats. We aimed to detect the genetic adaptation mechanisms of barnacles responding to the microhabitat changes in the intertidal zone based on comparative transcriptomics. …”
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Transcriptome sequencing and screening of anthocyanin related genes in purple potato tubers (Solanum tuberosum L.) by Xiaojuan Wu, Yanhong Ma, Peijie Wang, Juan Wu, Nan Li, Zhicheng Zhang, Rui Xie, Dan Wang, Hushuai Nie

“…Nevertheless, the regulation mechanism of anthocyanins in purple potato at different growth stages remain unclear. Results In this study, through using the high-throughput sequencing and systematic bioinformatics analysis, a total of 7,176 significantly different expressed genes (DEGs) were discovered from the purple potato Huasong 66 tubers at different developmental stages. …”
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Synthesis of transcriptomic studies reveals a core response to heat stress in abalone (genus Haliotis) by Roy Barkan, Ira Cooke, Sue-Ann Watson, Jan M. Strugnell

“…This study uses a standardized bioinformatic pipeline to reanalyze and compare publicly available RNA-seq datasets from different heat stress studies on abalone. Results Nine publicly available RNA-seq datasets from nine different heat-stress studies on abalone from seven different abalone species and three hybrids were included in the meta-analysis. …”
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Dual RNA-seq reveals transcriptome changes during Fusarium virguliforme-Trichoderma afroharzianum interactions. by Mirian F Pimentel, Leonardo F Rocha, Arjun Subedi, Jason P Bond, Ahmad M Fakhoury

“…This study focuses on elucidating the mechanisms underlying observed phenotypic differences among the T. afroharzianum isolates Th19A and Th4 during confrontation with Fusarium virguliforme by investigating differences in their transcriptome at different stages of interaction. …”
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Predicting antimicrobial mechanism-of-action from transcriptomes: A generalizable explainable artificial intelligence approach. by Josh L Espinoza, Chris L Dupont, Aubrie O'Rourke, Sinem Beyhan, Pavel Morales, Amy Spoering, Kirsten J Meyer, Agnes P Chan, Yongwook Choi, William C Nierman, Kim Lewis, Karen E Nelson

“…In addition, we deploy our methods on a recent E. coli transcriptomics dataset from a different strain and a Mycobacterium smegmatis metabolomics timeseries dataset showcasing exceptionally high performance; improving upon the performance metrics of the original publications. …”
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Genomic and transcriptomic landscapes of metastatic neuroendocrine neoplasms from distinct primary sites and their clinical implications by Kathleen Wee, Kevin C. Yang, David F. Schaeffer, Chen Zhou, Emily Leung, Xiaolan Feng, Janessa Laskin, Marco A. Marra, Jonathan M. Loree, Sharon M. Gorski

“…Here, we describe the genomic and transcriptomic landscapes of 28 metastatic NENs across different primary anatomical sites (PASs) and their potential clinical implications. …”
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Exploring the diversity of galls on Artemisia indica induced by Rhopalomyia species through morphological and transcriptome analyses by Seiji Takeda, Makiko Yoza, Sawako Ueda, Sakura Takeuchi, Akiteru Maeno, Tomoaki Sakamoto, Seisuke Kimura

“…Vasculature developed de novo within the galls, indicating active transport of nutrients between galls and the host plant. Each gall had a different pattern of vasculature and lignification, probably due to differences in the site of gall generation and the gall midge species. …”
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Transcriptomic and metabolomic analyses provide insights into the biosynthesis of chlorogenic acids in Lonicera macranthoides Hand.-Mazz. by Yuan Pan, Xiao Zhao, Xiao-Li Wu, Yu Wang, Jun Tan, Da-Xia Chen

“…In this study, metabolomics and transcriptomics were used to analyze the metabolic and transcriptional differences of two different cultivars closed bud type (Bt), and flowering type (Ft), as well as the effect of jasmonic acid methyl ester (MeJA) on chlorogenic acids (CGAs) biosynthesis. …”
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Flu‐CED: A comparative transcriptomics database of influenza virus‐infected human and animal models by Yue Wu, Jue Wang, Jing Xue, Zhiguang Xiang, Jianguo Guo, Lingjun Zhan, Qiang Wei, Qi Kong

“…Abstract Background The continuing emergence of influenza virus has highlighted the value of public databases and related bioinformatic analysis tools in investigating transcriptomic change caused by different influenza virus infections in human and animal models. …”
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Integrated transcriptomic and metabolomic analyses provide insights into defense against Colletotrichum fructicola in octoploid strawberries by Xiaohua Zou, Yun Bai, Ying Ji, Liqing Zhang, Qinghua Gao, Xianping Fang

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Age-Related Meat Flavor Precursors of Naturally Grazed Sunit Sheep: Metabolomics and Transcriptomics Approaches by Yajuan Huang, Xige He, Yunfei Han, Lu Chen, Xueting Yu, Jin Li, Xueyan Yun, Rina Sha, Gerelt Borjigin

“…This study elucidated the regulatory mechanisms of age-related meat flavor precursors in naturally grazed Sunit sheep of different ages (6, 18, and 30 months) by analyzing their metabolite and mRNA profiles. …”
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Genome-wide analysis of the BoBZR1 family genes and transcriptome analysis in Brassica oleracea by Muhammad Asad Ullah, Muhammad Hamza, Rozia Gull, Muhammad Shafiq, Abdul Wahid, Shahab Ahmad, Tayebeh Ahmadi, Mehdi Rahimi

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The Effect of Oral Care Product Ingredients on Oral Pathogenic Bacteria Transcriptomics Through RNA-Seq by Ping Hu, Sancai Xie, Baochen Shi, Cheryl S. Tansky, Benjamin Circello, Paul A. Sagel, Eva Schneiderman, Aaron R. Biesbrock

“…Combining multiple ingredients targeting different mechanisms might be more efficient than single ingredients in complex oral microbiomes.…”
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Immune transcriptomic analysis on COVID-19 patients with varying clinical presentations identifies severity markers by Abdallah Musa Abdallah, Hifzur Rahman Ansari, Muhammad Shuaib, Asmma Doudin, Hadi M. Yassine, Syed Shahab Ud Din Shah, Fayaz Ahmad Mir, Mohamed M. Emara, Abdel-Naser Elzouki, Farhan S. Cyprian

“…However, the host responses to COVID-19, including systemic inflammation and immunity against SARS-CoV-2, remain largely undefined across different disease states. Here, we performed global transcriptome profiling of 228 peripheral blood samples of COVID-19 patients with different clinical manifestations and subsequent clustering using an unsupervised algorithm. …”
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Comparative Study and Transcriptomic Analysis on the Antifungal Mechanism of Ag Nanoparticles and Nanowires Against Trichosporon asahii by Han M, Xia Z, Zou Y, Hu P, Zhang M, Yang X, Ma MG, Yang R

“…This work proves that silver nanomaterials with different morphologies have potential applications in fungus therapy such as T. asahii.Keywords: Ag, nanoparticles, nanowires, fungus, antifungal mechanism, Trichosporon asahii, transcriptomics…”
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Phylogeny and species delimitation of ciliates in the genus Spirostomum (class Heterotrichea) using single-cell transcriptomes by Shahed Uddin Ahmed Shazib, Auden Cote-L’Heureux, Ragib Ahsan, Sergio A. Muñoz-Gómez, JunMo Lee, Laura A. Katz, Mann Kyoon Shin

“…We also provide a workflow for reconstructing nuclear ribosomal RNA gene sequences from transcriptome sequences using a read mapping approach, and compare different mapping methods to reconstruct reliable contigs. …”
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Transcriptome analysis of multiple tissues in the Babylonia areolata reveals the distinct response to Vibrio tubiashii infection by Chen Dai, Dapeng Luo, Qingming Liu, Jing Cui, Haohan Mi, Zuhao Zhang, Zhigang Tu, Minghui Shen

“…However, research regarding the host immune response against infection in multiple tissues is limited. In this study, transcriptome sequencing technology was used to explore gene expression differences in the gills, hemolymphocytes, and hepatopancreas following Vibrio tubiashii infection. …”
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