Clonal Tracking in the Mouse Brain with Single-Cell RNA-Seq.

Area of Science:

• Developmental Biology
• Neuroscience
• Genetics

Background:

• Lineage tracing identifies cell progeny from a single progenitor.
• Mammalian brain development requires understanding cell fate and relationships.
• Current methods are limited in throughput and efficiency.

Purpose of the Study:

• To develop a high-throughput lineage tracing method for the mammalian brain.
• To enable parallel labeling of thousands of progenitor cells.
• To analyze lineage relations and cell types using single-cell RNA sequencing.

Main Methods:

• Generation of barcoded lentivirus for genetic labeling.
• Microinjection into embryonic mouse forebrain (day 9.5).
• Single-cell RNA sequencing (scRNA-seq) library preparation and custom data analysis.

Main Results:

• Achieved >100-fold higher throughput compared to sparse fluorophore labeling.
• Reduced animal usage by >10 times.
• Enabled detailed analysis of lineage relationships and cell types.

Conclusions:

• Genetic barcoding combined with scRNA-seq offers a powerful, efficient approach for mammalian brain lineage tracing.
• This method significantly advances the study of developmental processes and cell diversification.
• It provides a scalable and resource-efficient alternative to traditional lineage tracing techniques.