Clonal tracking using embedded viral barcoding and high-throughput sequencing.

Nature Protocols
Charles BramlettRong Lu

Abstract

Embedded viral barcoding in combination with high-throughput sequencing is a powerful technology with which to track single-cell clones. It can provide clonal-level insights into cellular proliferation, development, differentiation, migration, and treatment efficacy. Here, we present a detailed protocol for a viral barcoding procedure that includes the creation of barcode libraries, the viral delivery of barcodes, the recovery of barcodes, and the computational analysis of barcode sequencing data. The entire procedure can be completed within a few weeks. This barcoding method requires cells to be susceptible to viral transduction. It provides high sensitivity and throughput, and enables precise quantification of cellular progeny. It is cost efficient and does not require any advanced skills. It can also be easily adapted to many types of applications, including both in vitro and in vivo experiments.

References

Jun 28, 2002·Nucleic Acids Research·Andreas W Rüfer, Brian Sauer
Dec 1, 2007·Nature Methods·Manfred SchmidtChristof von Kalle
Mar 29, 2008·Cell Stem Cell·Brad DykstraConnie Eaves
Apr 10, 2008·PloS One·Adam WasserstromEhud Shapiro
Sep 24, 2008·The Journal of Experimental Medicine·Koen SchepersTon N M Schumacher
Jan 23, 2010·Blood·Alice GerritsLeonid V Bystrykh
Apr 7, 2012·Nature Protocols·Kristoffer WeberBoris Fehse
Jun 7, 2012·Nature Methods·Leonid V BystrykhGerald de Haan
Dec 18, 2013·Science·Tim WangEric S Lander
Dec 18, 2013·Science·Ophir ShalemFeng Zhang
Jan 28, 2014·Nature·Anne C RiosJane E Visvader
Jan 31, 2014·Nucleic Acids Research·Kerstin CornilsBoris Fehse
Jul 6, 2014·Experimental Hematology·Shalin H NaikLeïla Perié
Jul 27, 2014·Methods in Molecular Biology·Leonid V BystrykhEvgenia Verovskaya
Oct 9, 2014·Nature·Jianlong SunFernando D Camargo
Apr 5, 2016·Methods in Molecular Biology·Leonid V Bystrykh, Mirjam E Belderbos
Jan 24, 2017·Nature Reviews. Genetics·Mollie B WoodworthChristopher A Walsh
Mar 4, 2017·Scientific Reports·Lars ThieleckeKerstin Cornils
Aug 17, 2017·Nature·Weike PeiHans-Reimer Rodewald
Aug 11, 2018·Science·Reza KalhorGeorge M Church
Sep 7, 2018·Nature·Henry Lee-SixPeter J Campbell
Nov 1, 2018·Nature Methods·Justus M Kebschull, Anthony M Zador
Nov 6, 2018·Science Immunology·Chuanfeng WuCynthia E Dunbar
Nov 19, 2018·Experimental Hematology·Anne-Marie LyneLeïla Perié

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Citations

Dec 11, 2020·Journal of Mammary Gland Biology and Neoplasia·Mokryun BaekGloria V Echeverria
May 26, 2021·Nature Protocols·Samuele FerrariPietro Genovese
Oct 14, 2021·Molecular Medicine Reports·Mo-Yu WangHong-Wu Xin

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Methods Mentioned

BETA
PCR
transgenic
transfection
FACS
Assay
electrophoresis
flow cytometry
Illumina sequencing

Software Mentioned

Anaconda
genBaRcode
Polylox
Anaconda Prompt
library
R
Spyder
Visual C + Compiler
py
Python

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