Fig. 1: Identification of Arabidopsis hypocotyl cell types using 10x Chromium snRNA-seq.
From: Strigolactones optimise plant water usage by modulating vessel formation
a Sample collection pipeline. b UMAP plot of 10x Chromium snRNA-seq analysis using 2,061 Arabidopsis hypocotyl nuclei organised in 18 clusters obtained through unsupervised clustering analysis. Differentiation trajectory based on pseudo-time analysis originating from CSCs is shown by black lines in the right-bottom. A scheme of major hypocotyl cell types is shown in the top left corner. c, d Dot plot showing the expression of tissue-specific and stage-specific marker genes identified in previous scRNA-seq analyses8,9,71 (c) and previously characterised tissue-specific marker genes (d) in the identified clusters (y-axis, shared between c and d). The size of the circles represents the percentage of cells with expression (percent expressed), whereas the colour indicates the scaled average expression (average expression). XPa-dV xylem parenchyma and developing vessels, XP xylem parenchyma, CSC cambium stem cells, devP developing phloem, CC companion cells, PP phloem parenchyma, devC developing cortex, cortex-EPI cortex-epidermis. Source data are provided as a Source Data file.
