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bioRxiv · 10.1101/2021.12.02.470912

Smart3-ATAC: a highly sensitive method for joint accessibility and full-length transcriptome analysis in single cells

Cheng, H.·Pui, H.-P.·Lentini, A.·Kolbeinsdottir, S.·Andrews, N.·Pei, Y.·Reinius, B.·Deng, Q.·Enge, M.
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Abstract

Joint single-cell measurements of gene expression and DNA regulatory element activity holds great promise as a tool to understand transcriptional regulation. Towards this goal we have developed Smart3-ATAC, a highly sensitive method which allows joint mRNA and chromatin accessibility analysis genome wide in single cells. With Smart3-ATAC, we are able to obtain the highest possible quality measurements per cell. The method combines transcriptomic profiling based on the highly sensitive Smart-seq3 protocol on cytosolic mRNA, with a novel low-loss single-cell ATAC (scATAC) protocol to measure chromatin accessibility. Compared to current droplet multiome methods, the yield of both the scATAC protocol and mRNA-seq protocol is markedly higher.

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Cheng, H., Pui, H.-P., Lentini, A., Kolbeinsdottir, S., Andrews, N., Pei, Y., Reinius, B., Deng, Q., Enge, M.. 2021-12-03. Smart3-ATAC: a highly sensitive method for joint accessibility and full-length transcriptome analysis in single cells. https://doi.org/10.1101/2021.12.02.470912

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