Gene

Biology

Genome Biology

DNA sequencing

Computational biology

Genetics

Exome sequencing

Transcriptome

Genome

Sequence (biology)

RNA-Seq

Genomics

Single cell sequencing

Cell

Single-cell analysis

Human genetics

Gene expression

Phenotype

Genome biology

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.

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