STRT-seq-2i: dual-index 5′ single cell and nucleus RNA-seq on an addressable microwell array

Hochgerner, H.; Lannerberg, P.; Hodge, R.; Mikes, J.; Heskol, A.; Hubschle, H.; Lin, P.; Picelli, S.; La Manno, G.; Ratz, M.; Dunne, J.; Husain, S.; Lein, E.; Srinivasan, M.; Zeisel, A.; Linnarsson, S.

doi:10.1101/126268

bioRxiv · 10.1101/126268

STRT-seq-2i: dual-index 5′ single cell and nucleus RNA-seq on an addressable microwell array

Hochgerner, H.·Lannerberg, P.·Hodge, R.·Mikes, J.·Heskol, A.·Hubschle, H.·Lin, P.·Picelli, S.·La Manno, G.·Ratz, M.·Dunne, J.·Husain, S.·Lein, E.·Srinivasan, M.·Zeisel, A.·Linnarsson, S.

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Abstract

Single-cell RNA-seq has become routine for discovering cell types and revealing cellular diversity, but currently no high-throughput platform has been used successfully on archived human brain samples. We present STRT-seq-2i, an addressable 9600-microwell array platform, combining sampling by limiting dilution or FACS, with imaging and high throughput at competitive cost. We applied the platform to fresh single mouse cortical cells and to frozen post-mortem human cortical nuclei, matching the performance of a previous lower-throughput platform.

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Hochgerner, H., Lannerberg, P., Hodge, R., Mikes, J., Heskol, A., Hubschle, H., Lin, P., Picelli, S., La Manno, G., Ratz, M., Dunne, J., Husain, S., Lein, E., Srinivasan, M., Zeisel, A., Linnarsson, S.. 2017-04-20. STRT-seq-2i: dual-index 5′ single cell and nucleus RNA-seq on an addressable microwell array. https://doi.org/10.1101/126268

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