When DNA gets in the way: A cautionary note for DNA contamination in extracellular RNA-seq studies

Abstract

With great interest, we read the paper by Zhou et al. describing a methodology that enables extracellular RNA sequencing (exRNA-seq) from extremely low input (Small Input Liquid Volume Extracellular RNA Sequencing [SILVER-seq]). We were intrigued by the high number of detected genes compared to our previous studies and noticed low reproducibility. We hypothesized that these observations could originate from substantial DNA contamination. Therefore, we reanalyzed the SILVER-seq data to determine the extent of DNA signal in the sequencing reads.