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<p>RNA-seq experiments are a pivotal tool for plant stress research. However, the original experimental designers usually analyze the increasing amount of data in a contextualized manner. Although accumulating the data in public repositories is crucial, making it accessible in a rapid-consult format is desirable. Here, we release BrachyTonalli 1.0 (URL: <a href="http://shiny.unpa.edu.mx:3838/tonalli/">http://shiny.unpa.edu.mx:3838/tonalli/</a>), a Shiny web-based app to access and visualize the transcriptome data of two ecotypes of the model grass <i>Brachypodium distachyon</i> under low-light, submergence, and normal growth conditions across one diurnal cycle consisting of a total of 89 libraries of at least 10&#xa0;M sequences (total ~ 1800&#xa0;M). The information obtained includes abundance, fold change, inter-stress and ecotype comparisons, and false discovery rates for each gene explored. The graphs, individual, and full dataset are available to download. In addition to studying the aforementioned plant biology questions, we explored the use of BrachyTonalli for an out-of-scope application by proposing new housekeeping (constitutive) transcripts for <i>Brachypodium distachyon</i>.</p>

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BrachyTonalli 1.0: a Shiny web-based app to explore the transcriptome of Brachypodium distachyon ecotypes under low-light, submergence, and normal growth conditions

  • 期刊论文

  • 发表日期：

    2025年5月22日

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  • Julián Mario Peña-Castro,
  • Piyada Juntawong,
  • Blanca E. Barrera-Figueroa,
  • Lucisabel Medina-Chávez

摘要

RNA-seq experiments are a pivotal tool for plant stress research. However, the original experimental designers usually analyze the increasing amount of data in a contextualized manner. Although accumulating the data in public repositories is crucial, making it accessible in a rapid-consult format is desirable. Here, we release BrachyTonalli 1.0 (URL: http://shiny.unpa.edu.mx:3838/tonalli/), a Shiny web-based app to access and visualize the transcriptome data of two ecotypes of the model grass Brachypodium distachyon under low-light, submergence, and normal growth conditions across one diurnal cycle consisting of a total of 89 libraries of at least 10 M sequences (total ~ 1800 M). The information obtained includes abundance, fold change, inter-stress and ecotype comparisons, and false discovery rates for each gene explored. The graphs, individual, and full dataset are available to download. In addition to studying the aforementioned plant biology questions, we explored the use of BrachyTonalli for an out-of-scope application by proposing new housekeeping (constitutive) transcripts for Brachypodium distachyon.