Pérez-Rodríguez Daniel, Agís-Balboa Roberto Carlos, López-Fernández Hugo
Neuro Epigenetics Lab, Health Research Institute of Santiago de Compostela (IDIS), Santiago University Hospital Complex, 15706 Santiago de Compostela, Spain.
Translational Neuroscience Group, Galicia Sur Health Research Institute (IIS Galicia Sur), Área Sanitaria de Vigo-Hospital Álvaro Cunqueiro, SERGAS-UVIGO, CIBERSAM-ISCIII, 36213 Vigo, Spain.
Biomedicines. 2023 Apr 21;11(4):1230. doi: 10.3390/biomedicines11041230.
High-throughput sequencing of small RNA molecules such as microRNAs (miRNAs) has become a widely used approach for studying gene expression and regulation. However, analyzing miRNA-Seq data can be challenging because it requires multiple steps, from quality control and preprocessing to differential expression and pathway-enrichment analyses, with many tools and databases available for each step. Furthermore, reproducibility of the analysis pipeline is crucial to ensure that the results are accurate and reliable. Here, we present myBrain-Seq, a comprehensive and reproducible pipeline for analyzing miRNA-Seq data that incorporates miRNA-specific solutions at each step of the analysis. The pipeline was designed to be flexible and user-friendly, allowing researchers with different levels of expertise to perform the analysis in a standardized and reproducible manner, using the most common and widely used tools for each step. In this work, we describe the implementation of myBrain-Seq and demonstrate its capacity to consistently and reproducibly identify differentially expressed miRNAs and enriched pathways by applying it to a real case study in which we compared schizophrenia patients who responded to medication with treatment-resistant schizophrenia patients to obtain a 16-miRNA treatment-resistant schizophrenia profile.
对微小RNA（miRNA）等小RNA分子进行高通量测序已成为研究基因表达和调控的一种广泛使用的方法。然而，分析miRNA测序数据可能具有挑战性，因为它需要多个步骤，从质量控制和预处理到差异表达分析和通路富集分析，每个步骤都有许多工具和数据库可供使用。此外，分析流程的可重复性对于确保结果的准确性和可靠性至关重要。在这里，我们介绍了myBrain-Seq，这是一个用于分析miRNA测序数据的全面且可重复的流程，在分析的每个步骤都纳入了针对miRNA的解决方案。该流程设计得灵活且用户友好，使不同专业水平的研究人员能够使用每个步骤中最常用和广泛使用的工具，以标准化和可重复的方式进行分析。在这项工作中，我们描述了myBrain-Seq的实现，并通过将其应用于一个实际案例研究来展示其持续且可重复地识别差异表达miRNA和富集通路的能力，在该案例中，我们比较了对药物有反应的精神分裂症患者和难治性精神分裂症患者，以获得一个包含16种miRNA的难治性精神分裂症特征图谱。
