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Related Experiment Video

Updated: Nov 4, 2025

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues
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BAR-Seq clonal tracking of gene-edited cells.

Samuele Ferrari1,2, Stefano Beretta3, Aurelien Jacob3,4

  • 1San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy. ferrari.samuele@hsr.it.

Nature Protocols
|May 25, 2021
PubMed
Summary

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BAR-Seq is a new pipeline for tracking gene-edited cells, enabling detailed analysis of engineered clones. This method aids in understanding cell behavior and comparing gene editing strategies for therapeutic development.

Area of Science:

  • Molecular Biology
  • Genetics
  • Bioinformatics

Background:

  • Gene editing technologies offer precise genomic modification for gene therapy.
  • Limited clonal tracking methods hinder the study of engineered cell populations.
  • Understanding clone diversity and behavior is crucial for therapeutic applications.

Purpose of the Study:

  • To develop and present the BAR-Seq pipeline for clonal tracking of gene-edited cells.
  • To provide a user-friendly web application for analyzing sequencing data.
  • To enable detailed investigation of engineered clone dynamics.

Main Methods:

  • Development of a wet laboratory and bioinformatic pipeline (BAR-Seq).
  • Integration of a barcoding cassette via homology-directed targeted integration.

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  • Creation of an accessible web application for data analysis.

    • Main Results:

    • BAR-Seq enables clonal tracking of cells with targeted integration.
    • The BAR-Seq web application allows analysis of raw sequencing data without advanced skills.
    • The pipeline was successfully applied to study clonal dynamics in human edited hematopoietic stem/progenitor cells.

    Conclusions:

    • BAR-Seq provides a robust strategy for clonal tracking in gene editing research.
    • The tool facilitates the study of engineered cell biology in basic and translational research.
    • BAR-Seq allows for stringent comparison of gene editing protocols at the clonal level.