ArticlePeerJ2021
Effective ribosomal RNA depletion for single-cell total RNA-seq by scDASH.
Article in PeerJ, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
17 citing papers in PubMed, 28 citations in OpenAlex.
- Maternal obesity remodels nutrient transport transcriptional programs in early mouse embryonic and extraembryonic cell lineages.Molecular metabolism · 2026Article
- A practical guide to targeted single-cell RNA sequencing technologies.Communications biology · 2026Review
- Sensitive, flexible, and affordable serum RNA sequencing for pathogen detection on the Oxford Nanopore platform.BMC genomics · 2026Article
- The CRISPR-Cas toolkit for mosquito-borne virus surveillance: detection, tracing, and discovery.Frontiers in cellular and infection microbiology · 2026Review
- Harp: data harmonization for computational tissue deconvolution across diverse transcriptomics platforms.Bioinformatics (Oxford, England) · 2025Article
- Bronchopulmonary dysplasia with pulmonary hypertension associates with semaphorin signaling loss and functionally decreased FOXF1 expression.Nature communications · 2025Article
- A CRISPR/Cas9-based enhancement of high-throughput single-cell transcriptomics.Nature communications · 2025Article
- scTrends: A living review of commercial single-cell and spatial 'omic technologies.Cell genomics · 2024Review
- RAG-seq: NSR-primed and Transposase Tagmentation-mediated Strand-specific Total RNA Sequencing in Single Cells.Genomics, proteomics & bioinformatics · 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
- Respiratory epithelial cell types, states and fates in the era of single-cell RNA-sequencing.The Biochemical journal · 2023Review
- CRISPR/Cas9-based depletion of 16S ribosomal RNA improves library complexity of single-cell RNA-sequencing.bioRxiv : the preprint server for biology · 2023Article
- Article
- scONE-seq: A single-cell multi-omics method enables simultaneous dissection of phenotype and genotype heterogeneity from frozen tumors.Science advances · 2023Article
- Profiling Single-Cell Genome and Transcriptome by scONE-Seq.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Single-Cell RNA Sequencing with Spatial Transcriptomics of Cancer Tissues.International journal of molecular sciences · 2022Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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 the cost of sequencing non-messenger transcripts, such as ribosomal RNA (rRNA), that are usually not of-interest. Hence, there are not very many protocols that enable single-cell analysis of total RNA. We adapted a method called DASH (Depletion of Abundant Sequences by Hybridisation) to make it suitable for depleting rRNA sequences from single-cell total RNA-seq libraries. Our analyses show that our single-cell DASH (scDASH) method can effectively deplete rRNAs from sequencing libraries with minimal off-target non-specificity. Importantly, as a result of depleting the rRNA, the rest of the transcriptome is significantly enriched for detection.
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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.