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Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads
- Sasagawa, Yohei, Danno, Hiroki, Takada, Hitomi, Ebisawa, Masashi, Tanaka, Kaori, Hayashi, Tetsutaro, Kurisaki, Akira, Nikaido, Itoshi
- Genome biology 2018 v.19 no.1 pp. 29
- embryonic stem cells, gene expression, genes, sequence analysis, transcriptome
- 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 from in vitro embryonic stem cells and an in vivo stromal vascular fraction with a limited number of reads.