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Genome Biol. 2018 Mar 9;19(1):29. doi: 10.1186/s13059-018-1407-3.

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

Author information

1
Bioinformatics Research Unit, Advanced Center for Computing and Communication, RIKEN, Hirosawa 2-1, Wako, Saitama, Japan.
2
Laboratory of Stem Cell Technology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama-cho 8916-5, Ikoma, Nara, Japan.
3
Laboratory of Stem Cell Technology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama-cho 8916-5, Ikoma, Nara, Japan. akikuri@bs.naist.jp.
4
Bioinformatics Research Unit, Advanced Center for Computing and Communication, RIKEN, Hirosawa 2-1, Wako, Saitama, Japan. itoshi.nikaido@riken.jp.
5
Single-cell Omics Research Unit, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Japan. itoshi.nikaido@riken.jp.

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:

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

PMID:
29523163
PMCID:
PMC5845169
DOI:
10.1186/s13059-018-1407-3
[Indexed for MEDLINE]
Free PMC Article

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