SnFFPE-Seq: towards scalable single nucleus RNA-Seq of formalin-fixed paraffin-embedded (FFPE) tissue

Chung, H.; Melnikov, A.; McCabe, C.; Drokhlyansky, E.; Van Wittenberghe, N.; Magee, E. M.; Waldman, J.; Spira, A.; Chen, F.; Mazzilli, S.; Rozenblatt-Rosen, O.; Regev, A.

doi:10.1101/2022.08.25.505257

bioRxiv · 10.1101/2022.08.25.505257

SnFFPE-Seq: towards scalable single nucleus RNA-Seq of formalin-fixed paraffin-embedded (FFPE) tissue

Chung, H.·Melnikov, A.·McCabe, C.·Drokhlyansky, E.·Van Wittenberghe, N.·Magee, E. M.·Waldman, J.·Spira, A.·Chen, F.·Mazzilli, S.·Rozenblatt-Rosen, O.·Regev, A.

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Abstract

Profiling cellular heterogeneity in formalin-fixed paraffin-embedded (FFPE) tissues is key to characterizing clinical specimens for biomarkers, therapeutic targets, and drug responses. Here, we optimize methods for isolating intact nuclei and single nucleus RNA-Seq from FFPE tissues in the mouse brain, and demonstrate a pilot application to a human clinical specimen of lung adenocarcinoma. Our method opens the way to broad applications of snRNA-Seq to archival tissues, including clinical samples.

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Chung, H., Melnikov, A., McCabe, C., Drokhlyansky, E., Van Wittenberghe, N., Magee, E. M., Waldman, J., Spira, A., Chen, F., Mazzilli, S., Rozenblatt-Rosen, O., Regev, A.. 2022-08-25. SnFFPE-Seq: towards scalable single nucleus RNA-Seq of formalin-fixed paraffin-embedded (FFPE) tissue. https://doi.org/10.1101/2022.08.25.505257

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