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Efficient Ribosomal RNA Depletion From Drosophila Total RNA For Next-Generation Sequencing Applications

Koppaka, O.; Tandon, S.; Chodankar, A.; Pandit, A.; Bakthavachalu, B.

2024-11-28 molecular biology
10.1101/2024.11.28.625868 bioRxiv
Show abstract

We developed a cost-effective enzyme-based rRNA-depletion method tailored for Drosophila melanogaster, addressing the limitations of existing commercial kits and the lack of peer-reviewed alternatives. Our method employs single-stranded DNA probes complementary to Drosophila rRNA, forming DNA-RNA hybrids. These hybrids are then degraded using the RNase H enzyme, effectively removing rRNA and enriching all non-ribosomal RNAs, including mRNA, lncRNA and small RNA. When compared to a commercial rRNA removal kit, our approach demonstrated superior rRNA removal efficiency and mapping percentage, confirming its effectiveness. Additionally, our method successfully enriched the non-coding transcriptome, making it a valuable tool for studying ncRNA in Drosophila. The probe sequences and rRNA-depletion protocol are made freely available, offering a reliable alternative for rRNA-depletion experiments.

Published in Wellcome Open Research · training set

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