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

By Hannah Hochgerner, Peter Lännerberg, Rebecca Hodge, Jaromir Mikes, Abeer Heskol, Herman Hubschle, Philip Lin, Simone Picelli, Gioele La Manno, Michael Ratz, Jude Dunne, Syed Husain, Ed Lein, Maithreyan Srinivasan, Amit Zeisel, Sten Linnarsson

Posted 20 Apr 2017
bioRxiv DOI: 10.1101/126268 (published DOI: 10.1038/s41598-017-16546-4)

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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