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A simple, cost-effective, and robust method for rRNA depletion in RNA-sequencing studies

ABSTRACT: These experiments were designed to quantify depletion of rRNA sequencing reads from bacterial RNA-seq libraries and verify that mRNA sequencing reads were not altered. Specifically, we tested an rRNA depletion method using custom-designed biotinylated oligonucleotides and compared these results to undepleted (total RNA) libraries and libraries made with the previously-available Ribo-Zero kit (Illumina).

ORGANISM(S): Caulobacter vibrioides Escherichia coli Bacillus subtilis

PROVIDER: GSE142656 | GEO | 2019/12/28

REPOSITORIES: GEO

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A simple, cost-effective, and robust method for rRNA depletion in RNA-sequencing studies

Project description:A simple, cost-effective, and robust method for rRNA depletion in RNA-sequencing studies

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Project description: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.

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