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 Kaori Tanaka
A1 Tetsutaro Hayashi
A1 Akira Kurisaki
A1 Itoshi Nikaido
YR 2017
UL http://biorxiv.org/content/early/2017/12/28/159384.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 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 in total from in vitro embryonic stem cells and an in vivo stromal vascular fraction with a limited number of reads.UMIunique molecular identifierPCRpolymerase chain reactionPCCPearson’s correlation coefficientSCCSpearman’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 scatterTPRtrue positive rateDEGdifferentially expressed gene