Single-cell Quartz-Seq reveals fluctuations in global gene expression in a single cell type in the same cell-cycle phase. (a) The × and Y axes represent the standard deviation (SD) of gene expression from the different datasets from single-cell Quartz-Seq with single embryonic stem (ES) cells that were all in the G1 phase of the cell cycle (n = 12, n = 8). (b) We detected expression of nine genes (Fn1, Zfp42, Sgk1, Tfrc, Utf1, Lefty1, Nanog, Sox2, and Spp1) by amplification-free single-cell quantitative (q)PCR with single ES cells in the G1 phase.The nine genes were selected from the ES cell differentiated genes (ES: fragment per kilobase of transcript per million fragments sequenced (FPKM) > 2; PrE: FPKM < 1). The plot shows the gene expression for the single-cell analysis of ES (n = 96 single ES cells in the G1 phase of the cell cycle) and ESA samples (n = 48 'averaged' single-cell samples from 300 pooled ES cells in the G1 phase). The ES single-cell box plots represent the gene-expression variability that contains the biological variability and the experimental error, while the ESA sample box plots represent the gene-expression variability due to experimental error. (c) The × axis represents the coefficient of variation (CV) of the gene expression from single-cell Quartz-Seq data with single ES cells in the G1 phase of the cell cycle (n = 12). The Y axis represents the CV of the gene expression from amplification-free single-cell qPCR with ES cells in the G1 phase of the cell cycle (n = 96). The CVs of the gene expression are plotted for the nine genes. The red lines represent regressions.