ArticleNucleic acids research2019
CRISPR/Cas9-targeted removal of unwanted sequences from small-RNA sequencing libraries.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Systematic evaluation of 24 extraction and library preparation combinations for metagenomic sequencing of SARS-CoV-2 in saliva.bioRxiv : the preprint server for biology · 2026Article
- A population-scale atlas of blood and tissue in lupus nephritis.bioRxiv : the preprint server for biology · 2026Article
- The CRISPR-Cas toolkit for mosquito-borne virus surveillance: detection, tracing, and discovery.Frontiers in cellular and infection microbiology · 2026Review
- MUTE-Seq: An Ultrasensitive Method for Detecting Low-Frequency Mutations in cfDNA With Engineered Advanced-Fidelity FnCas9.Advanced materials (Deerfield Beach, Fla.) · 2025Article
- Evaluating the potential and limitations of nanopore adaptive sampling for targeted transcriptome sequencing.Genome biology · 2025Article
- A CRISPR/Cas9-based enhancement of high-throughput single-cell transcriptomics.Nature communications · 2025Article
- RAG-seq: NSR-primed and Transposase Tagmentation-mediated Strand-specific Total RNA Sequencing in Single Cells.Genomics, proteomics & bioinformatics · 2024Article
- SingmiR: a single-cell miRNA alignment and analysis tool.Nucleic acids research · 2024Article
- Depletion-assisted multiplexed cell-free RNA sequencing reveals distinct human and microbial signatures in plasma versus extracellular vesicles.Clinical and translational medicine · 2024Article
- CRISPR/Cas9-based depletion of 16S ribosomal RNA improves library complexity of single-cell RNA-sequencing in planarians.BMC genomics · 2023Article
- CRISPR/Cas9-based depletion of 16S ribosomal RNA improves library complexity of single-cell RNA-sequencing.bioRxiv : the preprint server for biology · 2023Article
- Blocking Abundant RNA Transcripts by High-Affinity Oligonucleotides during Transcriptome Library Preparation.Biological procedures online · 2023Article
- Low-input RNase footprinting for simultaneous quantification of cytosolic and mitochondrial translation.Genome research · 2022Article
- Single-cell microRNA sequencing method comparison and application to cell lines and circulating lung tumor cells.Nature communications · 2021Article
- Small RNA-Sequencing: Approaches and Considerations for miRNA Analysis.Diagnostics (Basel, Switzerland) · 2021Review
- Improved bacterial RNA-seq by Cas9-based depletion of ribosomal RNA reads.RNA (New York, N.Y.) · 2020Article
- Depletion of erythropoietic miR-486-5p and miR-451a improves detectability of rare microRNAs in peripheral blood-derived small RNA sequencing libraries.NAR genomics and bioinformatics · 2020Article
- Novel CRISPR-based sequence specific enrichment methods for target loci and single base mutations.PloS one · 2020Article
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Authors and funding
6 authors.
Funding
Abstract
In small RNA (smRNA) sequencing studies, highly abundant molecules such as adapter dimer products and tissue-specific microRNAs (miRNAs) inhibit accurate quantification of lowly expressed species. We previously developed a method to selectively deplete highly abundant miRNAs. However, this method does not deplete adapter dimer ligation products that, unless removed by gel-separation, comprise most of the library. Here, we have adapted and modified recently described methods for CRISPR/Cas9-based Depletion of Abundant Species by Hybridization ('DASH') to smRNA-seq, which we have termed miRNA and Adapter Dimer-DASH (MAD-DASH). In MAD-DASH, Cas9 is complexed with single guide RNAs (sgRNAs) targeting adapter dimer ligation products, alongside highly expressed tissue-specific smRNAs, for cleavage in vitro. This process dramatically reduces adapter dimer and targeted smRNA sequences, can be multiplexed, shows minimal off-target effects, improves the quantification of lowly expressed miRNAs from human plasma and tissue derived RNA, and obviates the need for gel-separation, greatly increasing sample throughput. Additionally, the method is fully customizable to other smRNA-seq preparation methods. Like depletion of ribosomal RNA for mRNA-seq and mitochondrial DNA for ATAC-seq, our method allows for greater proportional read-depth of non-targeted sequences.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.