Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads

Sasagawa, Y.; Danno, H.; Takada, H.; Ebisawa, M.; Hayashi, T.; Kurisaki, A.; Nikaido, I.

doi:10.1101/159384

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bioRxiv · 10.1101/159384

Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads

Sasagawa, Y.·Danno, H.·Takada, H.·Ebisawa, M.·Hayashi, T.·Kurisaki, A.·Nikaido, I.

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Abstract

High-throughput single-cell RNA-seq methods assign limited unique molecular identifier (UMI) counts as gene expression values to single cells from shallow sequence reads and detect limited gene counts. We thus developed a high-throughput single-cell RNA-seq method, Quartz-Seq2, to overcome these issues. Our improvements in the reaction steps make it possible to effectively convert initial reads to UMI counts (at a rate of 30%-50%) and detect more genes. To demonstrate the power of Quartz-Seq2, we analyzed approximately 10,000 transcriptomes in total from in vitro embryonic stem cells and an in vivo stromal vascular fraction with a limited number of reads.

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Sasagawa, Y., Danno, H., Takada, H., Ebisawa, M., Hayashi, T., Kurisaki, A., Nikaido, I.. 2017-07-05. Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads. https://doi.org/10.1101/159384

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