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Fig. 3 | Genome Biology

Fig. 3

From: Single-cell transcriptomic reconstruction reveals cell cycle and multi-lineage differentiation defects in Bcl11a-deficient hematopoietic stem cells

Fig. 3

Transcriptomic reconstruction of cell cycle progression by single-cell RNA-seq. a PCA of Bcl11a +/+ HSCs based on the expression of 2212 cell cycle-related genes annotated in the GO, Cyclebase database and Oki et al. [19]. The loading plot of the first two principal components is shown. Each point represents one HSC. b Subgrouping of Bcl11a +/+ HSCs by PCA. The Bcl11a +/+ HSCs were grouped into five different clusters (C1–5) based on their proximity in the PCA loading plot as in (a). c Hierarchical clustering and Pearson correlation heatmap of Bcl11a +/+ HSCs. Correlation between Bcl11a +/+ HSCs was estimated by the Pearson correlation coefficients. The column and row colors shown above and to the left correspond to the five subgroups by PCA as in (b). d PCA loading plots of Bcl11a +/+ HSCs as in (a) with expression of selected cell cycle stage-specific genes overlaid. The expression level was calculated as log10 (normalized counts +1). e The normalized enrichment scores of significantly enriched gene sets (p < 0.05, false discovery rate < 0.05) in the C3 cluster compared with the C1 cluster curated by the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. GSEA gene set enrichment analysis

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