TY - JOUR T1 - Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads JF - bioRxiv DO - 10.1101/159384 SP - 159384 AU - Yohei Sasagawa AU - Hiroki Danno AU - Hitomi Takada AU - Masashi Ebisawa AU - Tetsutaro Hayashi AU - Akira Kurisaki AU - Itoshi Nikaido Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/07/21/159384.abstract N2 - 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 ER -