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Fig. 5 | Genome Biology

Fig. 5

From: Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads

Fig. 5

High-throughput Quartz-Seq2 analysis of 4484 cells from mouse embryonic stem cells and differentiated cells. a We successfully analyzed 97.3% of 4608 wells. The procedures for cell suspension as used in this assay are shown. Cells cultured under ES-maintenance and Dex-treatment conditions were separately dissociated into single cells, stained with Hoechst 33,342 and/or Calcein-AM, and mixed evenly. Calcein-AM-positive and -negative cells were sorted to 384-well plates in a checkered pattern. White scale bars represent 100 μm. b Clustering of 4484 single cells according to the transcriptome. Plotting of cells on t-SNE space with color labeling for each cluster. The percentage indicates the proportion of cells for each cluster relative to all cells analyzed. Numbers in parentheses indicate the numbers of cells making up the cluster. c Marker genes for each cluster identified by Quartz-Seq2. Cluster-specific or cluster-enriched genes were calculated for each cluster, and their expression is displayed as a color in a heatmap. No more than 50 cells are shown for simplicity. d Reconstructed distribution of Calcein-AM intensity for each cluster. The x-axis represents the intensity of Calcein-AM dye staining. e Reconstructed distribution of Hoechst 33,342 intensity for each cluster. The y-axis represents the density of cells. The x-axis represents the intensity of Hoechst 33,342 dye staining

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