PT  - JOURNAL ARTICLE
AU  - Yohei Sasagawa
AU  - Hiroki Danno
AU  - Hitomi Takada
AU  - Masashi Ebisawa
AU  - Tetsutaro Hayashi
AU  - Akira Kurisaki
AU  - Itoshi Nikaido
TI  - Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads
AID  - 10.1101/159384
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 159384
4099  - http://biorxiv.org/content/early/2017/07/21/159384.short
4100  - http://biorxiv.org/content/early/2017/07/21/159384.full
AB  - 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.UMIunique molecular identifierPCRpolymerase chain reactionSCCSpearman’s rank correlation coefficientCVcoefficient of variationES cellembryonic stem cellPrE cellprimitive endoderm cellSVFstromal vascular fractionRTreverse-transcriptionDexdexamethasonePCAprincipal component analysisMSCmesenchymal stem cellTdTterminal deoxynucleotidyl transferaseGOGene OntologyFDRfalse discovery ratet-SNEt-distributed stochastic neighbor embeddingntnucleotidebpbase pairSSCside scatter