EFFICIENT RIBOSOMAL RNA DEPLETION FROM DROSOPHILA TOTAL RNA FOR NEXT-GENERATION SEQUENCING APPLICATIONS.

Q1 Medicine

Wellcome Open Research Pub Date : 2025-05-13 eCollection Date: 2025-01-01 DOI:10.12688/wellcomeopenres.23509.2

Omkar Koppaka, Shweta Tandon, Ankita Chodankar, Awadhesh Pandit, Baskar Bakthavachalu

引用次数: 0

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.

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从果蝇总RNA中高效提取核糖体RNA用于下一代测序应用。

我们开发了一种为果蝇量身定制的具有成本效益的基于酶的rrna耗尽方法，解决了现有商业试剂盒的局限性和缺乏同行评审的替代品。我们的方法使用与果蝇rRNA互补的单链DNA探针，形成DNA- rna杂交体。这些杂交种然后使用RNase H酶降解，有效地去除rRNA并富集所有非核糖体RNA，包括mRNA， lncRNA和小RNA。与商用rRNA去除试剂盒相比，我们的方法显示出更高的rRNA去除效率和作图百分比，证实了其有效性。此外，我们的方法成功地丰富了非编码转录组，使其成为研究果蝇ncRNA的有价值的工具。探针序列和rrna耗尽方案是免费提供的，为rrna耗尽实验提供了可靠的选择。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Wellcome Open Research Biochemistry, Genetics and Molecular Biology-Biochemistry, Genetics and Molecular Biology (all)

CiteScore

5.50

自引率

0.00%

发文量

426

审稿时长

1 weeks

期刊介绍： Wellcome Open Research publishes scholarly articles reporting any basic scientific, translational and clinical research that has been funded (or co-funded) by Wellcome. Each publication must have at least one author who has been, or still is, a recipient of a Wellcome grant. Articles must be original (not duplications). All research, including clinical trials, systematic reviews, software tools, method articles, and many others, is welcome and will be published irrespective of the perceived level of interest or novelty; confirmatory and negative results, as well as null studies are all suitable. See the full list of article types here. All articles are published using a fully transparent, author-driven model: the authors are solely responsible for the content of their article. Invited peer review takes place openly after publication, and the authors play a crucial role in ensuring that the article is peer-reviewed by independent experts in a timely manner. Articles that pass peer review will be indexed in PubMed and elsewhere. Wellcome Open Research is an Open Research platform: all articles are published open access; the publishing and peer-review processes are fully transparent; and authors are asked to include detailed descriptions of methods and to provide full and easy access to source data underlying the results to improve reproducibility.