Laboratory of Molecular Analysis (LAM), Department of Life Sciences, Federal University of Tocantins, UFT, University Campus of Palmas, Palmas, TO, 402-970, Brazil.
Computer Science Course, Federal University of Tocantins, University Campus of Palmas, Palmas, TO, Brazil.
BMC Genomics. 2024 Sep 30;25(1):907. doi: 10.1186/s12864-024-10808-y.
Gene expression through RT-qPCR can be performed by the relative quantification method, which requires the expression normalization through reference genes. Therefore, it is essential to validate, experimentally, the candidate reference genes. Thus, although there are several studies that are performed to identify the most stable reference genes, most them validate genes for very specific conditions, not exploring the whole potential of the research since not all possible combinations of treatments and/or conditions of the study are explored. For this reason, new experiments must be conducted by researchers that have interest in analyzing gene expression of treatments and/or conditions present, but not explored, in these studies. Here, we present the RGeasy tool, which aims to facilitate the selection of reference genes, allowing the user to choose genes for a greater number of combinations of treatments/conditions, compared to the ones present in the original articles, through just a few clicks. RGeasy was validated with RT-qPCR data from gene expression studies performed in two coffee species, Coffea arabica and Coffea canephora, and it can be used for any animal, plant or microorganism species. In addition to displaying a rank of the most stable reference genes for each condition or treatment, the user also has access to the primer pairs for the selected reference genes.
通过 RT-qPCR 进行基因表达可以采用相对定量方法，该方法需要通过参考基因进行表达归一化。因此，通过实验验证候选参考基因是至关重要的。因此，尽管有几项研究旨在鉴定最稳定的参考基因，但大多数研究仅针对特定条件验证基因，并未探索研究的全部潜力，因为并非所有可能的处理和/或条件组合都被探索过。出于这个原因，有兴趣分析研究中存在但未探索的处理和/或条件的基因表达的研究人员必须进行新的实验。在这里，我们介绍了 RGeasy 工具，其旨在方便参考基因的选择，使用户只需点击几下，就可以为更多处理/条件组合选择基因，而不是仅针对原始文章中存在的基因。我们使用在两种咖啡物种（阿拉比卡咖啡和卡内弗拉咖啡）中进行的基因表达研究的 RT-qPCR 数据对 RGeasy 进行了验证，并且它可以用于任何动物、植物或微生物物种。除了为每个条件或处理显示最稳定的参考基因的排名外，用户还可以访问所选参考基因的引物对。
