ArticleNature communications2025
A CRISPR/Cas9-based enhancement of high-throughput single-cell transcriptomics.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Targeted single-cell RNA and perturbation sequencing with TAP-seq.Nature protocols · 2026Review
- Sperm tRNA-derived fragments: molecular mechanisms and clinical implications for paternal epigenetic inheritance.Clinical epigenetics · 2026Review
- Comprehensive cellular analysis with single-nucleus RNA-seq of archived PAXgene whole blood samples.Cell reports methods · 2026Article
- A practical guide to targeted single-cell RNA sequencing technologies.Communications biology · 2026Review
- Review
- RoCK and ROI: single-cell transcriptomics with multiplexed enrichment of selected transcripts and region-specific sequencing.Nature communications · 2025Article
- CRISPR and Artificial Intelligence in Neuroregeneration: Closed-Loop Strategies for Precision Medicine, Spinal Cord Repair, and Adaptive Neuro-Oncology.International journal of molecular sciences · 2025Review
- A CRISPR/Cas9-based enhancement of high-throughput single-cell transcriptomics.Nature communications · 2025Article
- Long-read single-cell RNA sequencing enables the study of cancer subclone-specific genotypes and phenotypes in chronic lymphocytic leukemia.Genome research · 2025Article
- Long-read single-cell RNA sequencing enables the study of cancer subclone-specific genotype and phenotype in chronic lymphocytic leukemia.bioRxiv : the preprint server for biology · 2024Article
- Full-length isoform concatenation sequencing to resolve cancer transcriptome complexity.BMC genomics · 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
Corrections and comments
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Authors and funding
18 authors.
Funding
Abstract
Single-cell RNA-seq (scRNAseq) struggles to capture the cellular heterogeneity of transcripts within individual cells due to the prevalence of highly abundant and ubiquitous transcripts, which can obscure the detection of biologically distinct transcripts expressed up to several orders of magnitude lower levels. To address this challenge, here we introduce single-cell CRISPRclean (scCLEAN), a molecular method that globally recomposes scRNAseq libraries, providing a benefit that cannot be recapitulated with deeper sequencing. scCLEAN utilizes the programmability of CRISPR/Cas9 to target and remove less than 1% of the transcriptome while redistributing approximately half of reads, shifting the focus toward less abundant transcripts. We experimentally apply scCLEAN to both heterogeneous immune cells and homogenous vascular smooth muscle cells to demonstrate its ability to uncover biological signatures in different biological contexts. We further emphasize scCLEAN's versatility by applying it to a third-generation sequencing method, single-cell MAS-Seq, to increase transcript-level detection and discovery. Here we show the possible utility of scCLEAN across a wide array of human tissues and cell types, indicating which contexts this technology proves beneficial and those in which its application is not advisable.
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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.