RT Journal Article
SR Electronic
T1 Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 159384
DO 10.1101/159384
A1 Yohei Sasagawa
A1 Hiroki Danno
A1 Hitomi Takada
A1 Masashi Ebisawa
A1 Tetsutaro Hayashi
A1 Akira Kurisaki
A1 Itoshi Nikaido
YR 2017
UL http://biorxiv.org/content/early/2017/07/21/159384.abstract
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