# Transcript-guided targeted cell enrichment for scalable single-nucleus RNA sequencing

## TL;DR

EnrichSci is a new method for targeted single-nucleus RNA sequencing that enables detailed analysis of rare cell types and reveals aging-related gene and exon-level changes in the brain.

## Contribution

EnrichSci introduces a scalable, antibody-free platform combining FISH and combinatorial indexing for targeted single-nucleus RNA sequencing.

## Key findings

- EnrichSci uncovered aging-associated molecular dynamics in distinct oligodendrocyte subtypes.
- The method detected exon-level signatures linked to isoform switching and splicing factor dysregulation.
- It enables efficient profiling of rare cell types with full gene-body coverage.

## Abstract

Large-scale single-cell atlases have revealed many aging- and disease-associated cell types, yet these populations are often underrepresented in heterogeneous tissues, limiting detailed molecular analyses. To address this, we developed EnrichSci—a scalable, microfluidics-free platform that combines hybridization chain reaction RNA fluorescence in situ hybridization (FISH) with combinatorial indexing to profile single-nucleus transcriptomes of target cell types with full gene-body coverage. Applied to oligodendrocytes in the aging mouse brain, EnrichSci uncovered aging-associated molecular dynamics across distinct oligodendrocyte subtypes, revealing both shared and subtype-specific gene expression changes. Additionally, we identified aging-associated exon-level signatures missed by conventional gene-level analyses, highlighting post-transcriptional regulation as a critical dimension of cell-state dynamics in aging. By coupling transcript-guided enrichment with a scalable sequencing workflow, EnrichSci provides a versatile approach to decode dynamic regulatory landscapes in diverse cell types from complex tissues.

•EnrichSci enables antibody-free, targeted snRNA-seq of rare cell types•Efficient profiling captured age-related shifts in rare oligodendrocyte subtypes•EnrichSci detected gene- and exon-level expression changes in aged oligodendrocytes•Exon dynamics are linked to isoform switching and splicing factor dysregulation

EnrichSci enables antibody-free, targeted snRNA-seq of rare cell types

Efficient profiling captured age-related shifts in rare oligodendrocyte subtypes

EnrichSci detected gene- and exon-level expression changes in aged oligodendrocytes

Exon dynamics are linked to isoform switching and splicing factor dysregulation

EnrichSci is an antibody-free, targeted single-nucleus RNA sequencing method that enables efficient profiling of rare cell types with full gene-body coverage. Applied to oligodendrocytes in the brain, it uncovers aging-associated gene expression changes as well as exon-level dynamics that are linked to isoform switching and splicing factor dysregulation.