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Related Experiment Video

Updated: Dec 29, 2025

Genetic Barcoding with Fluorescent Proteins for Multiplexed Applications
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Quantifying Hematopoietic Stem Cell Clonal Diversity by Selecting Informative Amplicon Barcodes.

Emily M Teets1, Charles Gregory1, Jami Shaffer1

  • 1The Ohio State University College of Medicine, Department of Medicine, Division of Hematology, The Ohio State University Comprehensive Cancer Center, Ohio, USA.

Scientific Reports
|February 9, 2020
PubMed
Summary

This study introduces SABER, a new framework to identify unique genetic barcodes for quantifying hematopoietic stem cells (HSCs). SABER reliably measures HSC diversity, crucial for understanding aging and disease.

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Area of Science:

  • Stem cell biology
  • Genetics
  • Bioinformatics

Background:

  • Hematopoietic stem cells (HSCs) exhibit functional and genetic diversity, which declines with age and disease.
  • Existing methods for quantifying HSC diversity via genetic barcoding lack a framework for empirical barcode validation.

Purpose of the Study:

  • To develop and validate an analytical framework, SABER (Selection of informative Amplicon Barcodes from Experimental Replicates), for identifying unique amplicon barcodes.
  • To establish a method for reproducibly quantifying functional HSCs and their clonal diversity.

Main Methods:

  • Developed the SABER analytical framework to identify unique barcodes within large sets of experimental replicates.
  • Sequenced amplicon barcodes from 56 adult zebrafish blood samples, divided into training and validation sets.
  • Utilized bootstrapping to select samples with a high fraction of informative barcodes.

Main Results:

  • The SABER framework successfully identified informative barcodes.
  • The study found 4.2 ± 1.8 barcoded HSC clones per sample in the training set and 3.5 ± 2.1 in the validation set (p=0.3).
  • SABER demonstrated reproducible quantification of functional HSCs across different experimental group sizes.

Conclusions:

  • SABER provides a robust method for identifying informative amplicon barcodes, essential for quantifying HSC diversity.
  • This framework will advance large-scale studies investigating the mechanisms of HSC clonal evolution and age-related diversity loss.