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

Abstract

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.

Keywords

• High-throughput single-cell RNA-seq
• Flow cytometry
• Cell sorter
• Quartz-Seq
• Poly(A) tagging
• Stromal vascular fraction