Linking live-cell imaging to single-cell sequencing using genetic barcoding
- 1Hubrecht Institute KNAW, Oncode Institute, and University Medical Center Utrecht. 3584 CX Utrecht, The Netherlands
Abstract
Linking cellular phenotype to genotype and gene expression is a central goal in biomedical research. Live-cell imaging captures dynamic cellular phenotypes, whereas single-cell sequencing measures genome-wide molecular states, but pairing these readouts for the same cell remains challenging. Here we present Waldo, a genetically encoded single-cell barcoding strategy that can be read out by both live-cell imaging and single-cell sequencing to connect single cells across both modalities. Waldo barcodes are generated by combinatorial expression of synthetic cell-surface receptors, each detected by a cognate peptide probe coupled either to a fluorescent dye or a DNA barcode. Iterative fluorescent probe staining achieves large barcode diversity, while preserving fluorescence channels for phenotypic reporters. As a proof-of-principle, we use Waldo to link cell division phenotypes after chromosome missegregation to the karyotype and transcriptome of the same cells. Waldo provides a general strategy for connecting imaging phenotypes to genome-wide sequencing readouts in single cells.
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BibTeX
@misc{muller2026linking,
title = {{Linking live-cell imaging to single-cell sequencing using genetic barcoding}},
author = {M. Muller and S. J. A. Lochs and L. Apperloo and R. Banerjee and J. R. Fernandes Marques and C. Davo-Martinez and P. M. J. Rullens and M. Moreno-Gonzalez and V. Papageorgiou and B. A. Kramer and G. J. Kops and J. Kind and M. E. Tanenbaum},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.07.757257},
url = {https://www.biorxiv.org/content/10.64898/2026.10.07.757257v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Linking live-cell imaging to single-cell sequencing using genetic barcoding
AU - M. Muller
AU - S. J. A. Lochs
AU - L. Apperloo
AU - R. Banerjee
AU - J. R. Fernandes Marques
AU - C. Davo-Martinez
AU - P. M. J. Rullens
AU - M. Moreno-Gonzalez
AU - V. Papageorgiou
AU - B. A. Kramer
AU - G. J. Kops
AU - J. Kind
AU - M. E. Tanenbaum
PY - 2026
DA - 2026/10/07
PB - bioRxiv
DO - 10.64898/2026.10.07.757257
UR - https://www.biorxiv.org/content/10.64898/2026.10.07.757257v1
AB - Linking cellular phenotype to genotype and gene expression is a central goal in biomedical research. Live-cell imaging captures dynamic cellular phenotypes, whereas single-cell sequencing measures genome-wide molecular states, but pairing these readouts for the same cell remains challenging. Here we present Waldo, a genetically encoded single-cell barcoding strategy that can be read out by both live-cell imaging and single-cell sequencing to connect single cells across both modalities. Waldo barcodes are generated by combinatorial expression of synthetic cell-surface receptors, each detected by a cognate peptide probe coupled either to a fluorescent dye or a DNA barcode. Iterative fluorescent probe staining achieves large barcode diversity, while preserving fluorescence channels for phenotypic reporters. As a proof-of-principle, we use Waldo to link cell division phenotypes after chromosome missegregation to the karyotype and transcriptome of the same cells. Waldo provides a general strategy for connecting imaging phenotypes to genome-wide sequencing readouts in single cells.
ER -