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

Genome Biology

Tetsutaro Hayashi¹  Itoshi Nikaido¹  Masashi Ebisawa¹  Yohei Sasagawa¹  Hiroki Danno¹  Kaori Tanaka¹  Hitomi Takada²  Akira Kurisaki² 

[1] Bioinformatics Research Unit, Advanced Center for Computing and Communication, RIKEN;Laboratory of Stem Cell Technology, Graduate School of Biological Sciences, Nara Institute of Science and Technology;

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

DOI  :  10.1186/s13059-018-1407-3

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown