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

• Main Authors: Yohei Sasagawa, Hiroki Danno, Hitomi Takada, Masashi Ebisawa, Kaori Tanaka, Tetsutaro Hayashi, Akira Kurisaki, Itoshi Nikaido
• Format: Article
• Language: English
• Published: BMC 2018-03-01
• Series: Genome Biology
• Subjects: High-throughput single-cell RNA-seq; Flow cytometry; Cell sorter; Quartz-Seq; Poly(A) tagging; Stromal vascular fraction
• Online Access: http://link.springer.com/article/10.1186/s13059-018-1407-3

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 from in vitro embryonic stem cells and an in vivo stromal vascular fraction with a limited number of reads.