ArticleNature genetics2025
Transcript-specific enrichment enables profiling of rare cell states via single-cell RNA sequencing.
Article in Nature genetics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Asymmetric Evolution of Antennal Cell Types Underlies a Derived Ammonia-Sensing Logic for Ecological Adaptation in Bactrocera dorsalis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Cancer drug response and resistance: molecular mechanisms and combating strategies.Signal transduction and targeted therapy · 2026Review
- Adapted Smart-seq3xpress Facilitates Selective Microglial Transcriptomic Profiling From Frozen Brain Tissue.Cellular and molecular neurobiology · 2026Article
- Single-cell and spatial profiling in cancer biology and clinical oncology.Nature cancer · 2026Review
- Transcript-guided targeted cell enrichment for scalable single-nucleus RNA sequencing.Cell genomics · 2026Article
- A practical guide to targeted single-cell RNA sequencing technologies.Communications biology · 2026Review
- Genome-wide single-cell perturbation screens with VIPerturb-seq.bioRxiv : the preprint server for biology · 2026Article
- PURE-seq integrates FACS and PIP-seq for single-cell genomics of ultra-rare cells.Nature communications · 2026Article
- Liver single-nucleus multiome profiling reveals cell-type mechanisms for cardiometabolic traits.American journal of human genetics · 2026Article
- Single-cell transcriptomics of granulocytes in asthma and atopic diseases.Frontiers in molecular biosciences · 2026Review
- Methodologies for Sample Multiplexing and Computational Deconvolution in Single-Cell Sequencing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Robust self-supervised machine learning for single cell embeddings and annotations.bioRxiv : the preprint server for biology · 2025Article
- Unveiling heterogeneity in rare cells by combining RNA-based sorting and scRNA-seq.Nature genetics · 2025Article
- Spatial and single-cell transcriptomics capture two distinct cell states in soybean defense response toFrontiers in plant science · 2025Article
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15 authors.
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Abstract
Single-cell genomics technologies have accelerated our understanding of cell-state heterogeneity in diverse contexts. Although single-cell RNA sequencing identifies rare populations that express specific marker transcript combinations, traditional flow sorting requires cell surface markers with high-fidelity antibodies, limiting our ability to interrogate these populations. In addition, many single-cell studies require the isolation of nuclei from tissue, eliminating the ability to enrich learned rare cell states based on extranuclear protein markers. In the present report, we addressed these limitations by developing Programmable Enrichment via RNA FlowFISH by sequencing (PERFF-seq), a scalable assay that enables scRNA-seq profiling of subpopulations defined by the abundance of specific RNA transcripts. Across immune populations (n = 184,126 cells) and fresh-frozen and formalin-fixed, paraffin-embedded brain tissue (n = 33,145 nuclei), we demonstrated that programmable sorting logic via RNA-based cytometry can isolate rare cell populations and uncover phenotypic heterogeneity via downstream, high-throughput, single-cell genomics analyses.
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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.