Extended Data Fig. 9: Single cell RNA-seq analysis combined with ratiometric iFlpMosaics uncovers the combined NOTCH1/2/3 receptors cell-autonomous function in diverse embryo cell types. | Nature Methods

Extended Data Fig. 9: Single cell RNA-seq analysis combined with ratiometric iFlpMosaics uncovers the combined NOTCH1/2/3 receptors cell-autonomous function in diverse embryo cell types.

From: iFlpMosaics enable the multispectral barcoding and high-throughput comparative analysis of mutant and wild-type cells

Extended Data Fig. 9: Single cell RNA-seq analysis combined with ratiometric iFlpMosaics uncovers the combined NOTCH1/2/3 receptors cell-autonomous function in diverse embryo cell types.

a, Umaps and barplots showing the identified clusters and their frequencies among MYFP+ (Notch1/2/3WT) and MTomato+ (Notch1/2/3KO) cells. Dot plots showing the frequency (size) and expression level (color intensity) for the top cluster marker genes. b, Top differentially expressed genes per cluster between MYFP+ (Notch1/2/3WT) and MTomato+ (Notch1/2/3KO) cells. Dot plots also show the expression of Notch1 (note that Notch2 and Notch3 3′mRNA is still expressed after deletion and detected by scRNAseq, as shown in Fig. 6k), its canonical target genes (Hes and Hey, these are also regulated by other pathways), and the proliferation markers Ki67 (labels cells in G2/M of the cell-cycle) and Cdkn1a (likely arrested cells). c, Gene set enrichment analysis (GSEA) pathways with their normalized enrichment score.

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