RGeasy: a reference gene analysis tool for gene expression studies via RT-qPCR

• Published in: BMC genomics Vol. 25; no. 1; pp. 907 - 12
• Main Authors: de Souza, Micaele Rodrigues, Araújo, Ivo Pontes, da Costa Arruda, Wosley, Lima, André Almeida, Ságio, Solange Aparecida, Chalfun-Junior, Antonio, Barreto, Horllys Gomes
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 30-09-2024; BioMed Central; BMC
• Subjects: Algorithms; Analysis; Anopheles; Coffea - genetics; Coffea arabica; Coffea canephora; Coffee; Control; Efficiency; Endogenous genes; Examinations; Gene expression; Gene Expression Profiling - methods; Gene Expression Profiling - standards; Gene Expression Regulation, Plant; Genes; Genes, Plant; Identification and classification; Microorganisms; Normalization; Polymerase chain reaction; Real-Time Polymerase Chain Reaction - methods; Real-Time Polymerase Chain Reaction - standards; Reference Standards; Relative expression; Software; Testing; Validation studies; Validity; Brazil; Endogenous genes; Relative expression; Normalization
• ISSN: 1471-2164; 1471-2164
• 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.