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A Combinatorial Single-cell Approach to Characterize the Molecular and Immunophenotypic Heterogeneity of Human Stem and Progenitor Populations

A Combinatorial Single-cell Approach to Characterize the Molecular and Immunophenotypic Heterogeneity of Human Stem and Progenitor Populations

Published on: October 25, 2018

HybriSeq: probe-based device-free single-cell RNA profiling.

Daniel Foyt¹, David Brown², Shuqin Zhou²

¹UCSF-UC Berkeley Joint Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA.

Communications Biology

|August 19, 2025

Summary

This summary is machine-generated.

We developed HybriSeq, a new method for single-cell RNA profiling. This technique offers high sensitivity and unbiased transcript analysis, revealing cellular differences and improving gene annotation.

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Area of Science:

Molecular Biology
Genomics
Biotechnology

Background:

Single-cell RNA sequencing (scRNA-seq) is crucial for understanding cellular heterogeneity.
Existing methods may face limitations in sensitivity, transcript coverage, or bias.
Targeted RNA profiling is needed for in-depth analysis of specific gene sets.

Purpose of the Study:

To introduce and validate HybriSeq, a novel method for targeted single-cell RNA profiling.
To demonstrate HybriSeq's capability for high-sensitivity RNA detection and full-length transcript analysis.
To showcase HybriSeq's utility in characterizing cell-to-cell gene expression variability and transcript annotation.

Main Methods:

HybriSeq combines in situ hybridization with multiple probes for targeted RNA detection.
Split-pool barcoding is employed for sample multiplexing.
Sequencing analysis of probes enables transcript profiling.

Main Results:

HybriSeq achieves high sensitivity in detecting RNA targets using multiple probes.
The method provides unbiased profiling of entire transcripts, avoiding end bias.
HybriSeq successfully characterized cell-to-cell heterogeneity for 196 genes in peripheral blood mononuclear cells.
The approach identified previously missed transcript annotations.

Conclusions:

HybriSeq is a sensitive and unbiased method for targeted single-cell RNA profiling.
This technique enhances the characterization of cellular heterogeneity and transcript annotation.
HybriSeq offers a valuable tool for transcriptomic studies in various biological contexts.