Transcript-specific enrichment enables profiling rare cell states via scRNA-seq.

Area of Science:

• Single-cell genomics
• Molecular biology
• Biotechnology

Background:

• Single-cell RNA sequencing (scRNA-seq) reveals cell-state heterogeneity but struggles to isolate rare cell populations.
• Traditional cell sorting requires cell surface markers, limiting studies using isolated nuclei or lacking specific antibodies.
• Existing methods cannot enrich rare cells based on intracellular RNA markers.

Approach:

• Introduced Programmable Enrichment via RNA Flow-FISH by sequencing (PERFF-seq), a scalable assay for RNA-based cell sorting.
• PERFF-seq enables single-cell RNA sequencing (scRNA-seq) of subpopulations defined by specific RNA transcripts.
• Demonstrated PERFF-seq on immune cells and brain tissue nuclei, validating its sorting logic.

Key Points:

• PERFF-seq enriches rare cell populations based on RNA transcript presence or absence.
• The assay is compatible with both intact cells and isolated nuclei.
• Successfully applied PERFF-seq to large datasets of immune cells and brain nuclei.

Conclusions:

• PERFF-seq overcomes limitations of traditional sorting for rare cell population enrichment.
• This RNA-based cytometry method facilitates high-throughput scRNA-seq of targeted subpopulations.
• Provides a programmable and rational approach for studying rare cells identified by RNA markers.