CARLIN: A Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression.

Area of Science:

• Developmental Biology
• Genetics
• Molecular Biology

Background:

• Cell lineage tracing is crucial for understanding development and disease.
• Existing methods often lack the resolution or flexibility for dynamic studies.
• The CRISPR-activated repair lineage tracing (CARLIN) mouse line was developed to address these limitations.

Purpose of the Study:

• To detail protocols for maintaining and utilizing the CARLIN mouse line.
• To enable high-resolution, inducible cell lineage tracing in vivo.
• To facilitate simultaneous interrogation of lineage and gene expression from single cells.

Main Methods:

• Maintaining CARLIN mouse colonies.
• Inducible barcoding strategy using CRISPR technology.
• Amplification of CARLIN barcodes from DNA, RNA, and scRNA-seq libraries.
• Next-generation sequencing for barcode analysis.

Main Results:

• The CARLIN system allows for precise, time-controlled lineage labeling.
• Simultaneous capture of lineage and gene expression data from individual cells.
• Robust barcode amplification protocols for diverse sample types.

Conclusions:

• The CARLIN mouse line provides a powerful tool for high-resolution in vivo lineage tracing.
• This inducible system enhances flexibility for studying cellular dynamics across development and adulthood.
• The detailed protocols facilitate the application of CARLIN for diverse research questions in developmental biology and beyond.