Transcriptome of radially growing Arabidopsis wild type and d14 mutant hypocotyls with single cell resolution revealed by nucleus RNA-seq using 10x Chomium and VASA-seq

Wood formation is fundamental for the remarkable growth of plant bodies by continuously providing cells for long-distance transport of water and nutrients and for mechanical support. Vessel elements, the water transporting units within woody tissues, are generated from a cylindrical domain of cambium stem cells (CSCs) generating different vascular cell types in a bidirectional manner during the radial (secondary) growth. However, knowledge on the regulation of CSC activity is limited with unclear cell fate trajectories as the most obscure aspect in this context. Here, we provide a transcriptome atlas of CSCs and their derivatives at single cell resolution in Arabidopsis thaliana hypocotyl. Overall design: Nuclei of Arabidopsis thaliana (wild type, PXY:H4-GFP;SMXL5:H2B-RFP) hypocotyls were isolated by Fluorescence-activated nucleus sorting (FANS) based on Hoechst staining and analyzed using snRNAseq by the 10x Genomics pipeline (Library: DSNucseq2). Furthermore, VASA-seq analyses in 384-well plate format were applied to nuclei from whole hypocotyls (three replicate plates, Library: UHE-DS-v011, 012, 013) and cambium enriched nuclei (three replicate plates, Library: UHE-DS-v008, v009, v010) according to the GFP and RFP signal of nuclei during FANS (GFP+ and/or RFP+ nuclei). In addition, hypocotyl nuclei of wild type and d14-1 mutants were isolated and analyzed using snRNAseq by the 10x Genomics pipeline (Library: WT, d14).