ArticleProceedings of the National Academy of Sciences of the United States of America2020
HyPR-seq: Single-cell quantification of chosen RNAs via hybridization and sequencing of DNA probes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 43 citations in OpenAlex.
- Embryo-scale Visual Cell Sorting reveals a conserved transcriptomic signature of nucleolar size linked to proteostasis.bioRxiv : the preprint server for biology · 2026Article
- Genotype-to-Phenotype Mapping of Somatic Clonal Mosaicism via Single-Cell Co-Capture of DNA Mutations and mRNA Transcripts.Cancer discovery · 2026Article
- A practical guide to targeted single-cell RNA sequencing technologies.Communications biology · 2026Review
- RoCK and ROI: single-cell transcriptomics with multiplexed enrichment of selected transcripts and region-specific sequencing.Nature communications · 2025Article
- HybriSeq: probe-based device-free single-cell RNA profiling.Communications biology · 2025Article
- Article
- Single cell RNA sequencing after moderate traumatic brain injury: effects of therapeutic hypothermia.Journal of neuroinflammation · 2025Article
- Article
- Transcript-specific enrichment enables profiling of rare cell states via single-cell RNA sequencing.Nature genetics · 2025Article
- cfDiffusion: diffusion-based efficient generation of high quality scRNA-seq data with classifier-free guidance.Briefings in bioinformatics · 2024Article
- Concepts and new developments in droplet-based single cell multi-omics.Trends in biotechnology · 2024Review
- Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements.Nature communications · 2024Article
- Approaches to probe and perturb long noncoding RNA functions in diseases.Current opinion in genetics & development · 2024Review
- Transcript-specific enrichment enables profiling rare cell states via scRNA-seq.bioRxiv : the preprint server for biology · 2024Article
- Article
- CRISPR screening in hematology research: from bulk to single-cell level.Journal of hematology & oncology · 2023Review
- Functional characterization of Alzheimer's disease genetic variants in microglia.Nature genetics · 2023Article
- Light-Seq: light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing.Nature methods · 2022Article
- High-throughput CRISPRi and CRISPRa technologies in 3D genome regulation for neuropsychiatric diseases.Human molecular genetics · 2022Review
- Optimization of library preparation based on SMART for ultralow RNA-seq in mice brain tissues.BMC genomics · 2021Article
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Authors and funding
18 authors at 1 institution in 2 countries.
Funding
Abstract
Single-cell quantification of RNAs is important for understanding cellular heterogeneity and gene regulation, yet current approaches suffer from low sensitivity for individual transcripts, limiting their utility for many applications. Here we present Hybridization of Probes to RNA for sequencing (HyPR-seq), a method to sensitively quantify the expression of hundreds of chosen genes in single cells. HyPR-seq involves hybridizing DNA probes to RNA, distributing cells into nanoliter droplets, amplifying the probes with PCR, and sequencing the amplicons to quantify the expression of chosen genes. HyPR-seq achieves high sensitivity for individual transcripts, detects nonpolyadenylated and low-abundance transcripts, and can profile more than 100,000 single cells. We demonstrate how HyPR-seq can profile the effects of CRISPR perturbations in pooled screens, detect time-resolved changes in gene expression via measurements of gene introns, and detect rare transcripts and quantify cell-type frequencies in tissue using low-abundance marker genes. By directing sequencing power to genes of interest and sensitively quantifying individual transcripts, HyPR-seq reduces costs by up to 100-fold compared to whole-transcriptome single-cell RNA-sequencing, making HyPR-seq a powerful method for targeted RNA profiling in single cells.
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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.