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

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.

SUBMITTER: Sasagawa Y

PROVIDER: S-EPMC5845169 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature

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

Sasagawa Yohei Y Danno Hiroki H Takada Hitomi H Ebisawa Masashi M Tanaka Kaori K Hayashi Tetsutaro T Kurisaki Akira A Nikaido Itoshi I

Genome biology 20180309 1

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 ...[more]

PMID: 29523163

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

Project description: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 several of the reaction steps of Quartz-Seq2 allow us to effectively convert initial reads to UMI counts (at a rate of 30%–50%). To demonstrate the power of Quartz-Seq2, we analyzed transcriptomes from a cell population of in vitro embryonic stem cells and an in vivo stromal vascular fraction with a limited number of sequence reads. Preprint: http://www.biorxiv.org/content/early/2017/07/21/159384

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