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Sci Rep. 2017 Nov 27;7(1):16327. doi: 10.1038/s41598-017-16546-4.

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

Author information

1
Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
2
Science for Life Laboratory, Solna, Sweden.
3
Allen Institute for Brain Science, Seattle, Washington, USA.
4
WaferGen Biosystems Inc., Fremont, California, USA.
5
Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
6
Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden. amit.zeisel@ki.se.
7
Science for Life Laboratory, Solna, Sweden. amit.zeisel@ki.se.
8
Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden. sten.linnarsson@ki.se.
9
Science for Life Laboratory, Solna, Sweden. sten.linnarsson@ki.se.

Abstract

Single-cell RNA-seq has become routine for discovering cell types and revealing cellular diversity, but archived human brain samples still pose a challenge to current high-throughput platforms. 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 while retaining a high degree of flexibility, potentially also for other high-throughput applications.

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