Fig. 6: Cell-type-specific function of PIFs.
a, Visualization of shoot cell types via UMAP for dark-grown WT. Cell types are colour coded. Annotations for each cell type are indicated. b, Visualization of shoot cell types via UMAP for dark-grown pifq mutant. Cell types are colour coded. Annotations for each cell type are indicated. c,d, Visualization of shoot cell types via UMAP by integration of WT and pifq atlas with Dark sample in the de-etiolating shoot atlas after batch-effect correction. Cell types are annotated for WT and pifq. The corresponding cell types are set in the same column. e, Correlation analyses for different cell types in WT and pifq with whole-genome expression patterns. The expression ratio (the number of cells where the gene is transcribed/the total number of cells) for each gene in each cell type was calculated and used for Pearson correlation analyses. Cell-type pairs highly correlated in two samples are indicated by green squares. Cell-type clusters without highly correlated pairs are indicated by purple and blue squares. f,g, GO enrichment results for down- (f) and upregulated (g) genes in cell type clusters surrounded by the blue square. h, The expression patterns of PIF direct target genes in different cell types of dark-grown WT and pifq shoot tissues. A cluster of targets with similar patterns in most cell types but highly expressed in endodermal cells are enclosed in blue rectangles. i,j, The development trajectory of epidermal cells for dark-grown WT and the pifq mutant. Corresponding samples (i) and pseudotime inferred by expression (j) are indicated by different colours. k, The expression of PIF direct target genes during guard cell development. PIF direct target genes with significant expression difference during guard cell development are identified. Relative expression levels of these genes for cells sorted by pseudotime are illustrated. The values of log2(fold change) (expression in the pifq mutant/expression in WT) calculated with bulk RNA-seq data are supplied on the right.
