A protocol for identifying universal reference genes within a genus based on RNA-Seq data: a case study of poplar stem gene expression.

ABSTRACT: Real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) plays a crucial role in relative gene expression analysis, and accurate normalization relies on suitable reference genes (RGs). In this study, a pipeline for identifying candidate RGs from publicly available stem-related RNA-Seq data of different Populus species under various developmental and abiotic stress conditions is presented. DESeq2's median of ratios yielded the smallest coefficient of variance (CV) values in a total of 292 RNA-Seq samples and was therefore chosen as the method for sample normalization. A total of 541 stably expressed genes were retrieved based on the CV values with a cutoff of 0.3. Universal gene-specific primer pairs were designed based on the consensus sequences of the orthol

SUBMITTER: Xie Q 

PROVIDER: S-EPMC11524287 | biostudies-literature | 2024

REPOSITORIES: biostudies-literature