Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
Genome Biol. 2021 Apr 29;22(1):121. doi: 10.1186/s13059-021-02337-8.
Advances in transcriptome sequencing allow for simultaneous interrogation of differentially expressed genes from multiple species originating from a single RNA sample, termed dual or multi-species transcriptomics. Compared to single-species differential expression analysis, the design of multi-species differential expression experiments must account for the relative abundances of each organism of interest within the sample, often requiring enrichment methods and yielding differences in total read counts across samples. The analysis of multi-species transcriptomics datasets requires modifications to the alignment, quantification, and downstream analysis steps compared to the single-species analysis pipelines. We describe best practices for multi-species transcriptomics and differential gene expression.
转录组测序技术的进步使得能够从单个 RNA 样本中同时检测来自多个物种的差异表达基因，这种方法被称为双物种或多物种转录组学。与单物种差异表达分析相比，多物种差异表达实验的设计必须考虑到样本中每个感兴趣的生物体的相对丰度，通常需要富集方法，并导致样本之间的总读计数存在差异。与单物种分析流程相比，多物种转录组数据集的分析需要对比对、定量和下游分析步骤进行修改。我们描述了多物种转录组学和差异基因表达的最佳实践。
