Direct, high-throughput linking of single cell imaging and gene expression

Xu, C. K.; Meisl, G.; Moshkov, N.; Goda, K.; Shkarin, A.; Schlögel, M. F.; Knowles, T. P.; Mazutis, L.; Guck, J.

doi:10.1101/2025.09.01.672798

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bioRxiv · 10.1101/2025.09.01.672798

Direct, high-throughput linking of single cell imaging and gene expression

Xu, C. K.·Meisl, G.·Moshkov, N.·Goda, K.·Shkarin, A.·Schlögel, M. F.·Knowles, T. P.·Mazutis, L.·Guck, J.

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Abstract

Understanding sequence-phenotype relationships in biology requires large-scale datasets that provide one-to-one mapping of sequence to phenotype. Here, we address this challenge by introducing multimodal droplet barcoding, enabling individual microfluidic droplets to be tracked across both optical and sequencing measurements. We demonstrate the power of this approach through multimodal single-cell analysis. We pair imaging with gene expression profiling of individual cells, identifying genes that correlate with phenotypic features.

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Xu, C. K., Meisl, G., Moshkov, N., Goda, K., Shkarin, A., Schlögel, M. F., Knowles, T. P., Mazutis, L., Guck, J.. 2025-09-01. Direct, high-throughput linking of single cell imaging and gene expression. https://doi.org/10.1101/2025.09.01.672798

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