Effective ribosomal RNA depletion for single-cell total RNA-seq by scDASH

A decade since its invention, single-cell RNA sequencing (scRNA-seq) has become a mainstay technology for profiling transcriptional heterogeneity in individual cells. Yet, most existing scRNA-seq methods capture only polyadenylated mRNA to avoid expending resources on profiling the types of transcripts that are usually not-of-interest, such as ribosomal RNA (rRNA). Hence, protocols that enable analysis of the whole transcriptome remain scarce. We adapted a method called DASH (Depletion of Abundant Sequences by Hybridisation) for rRNA depletion from single-cell total RNA-seq libraries. Our analyses show that with our single-cell DASH (scDASH), rRNAs are effectively depleted with minimal non-specificity. Importantly, the rest of the transcriptome is significantly enriched for detection as a result of liberated sequencing quota from depleted rRNA. There are 8 single-cell and 4 min-bulk RNA-seq samples, with half of which subjected to rRNA depletion using scDASH.