Single nuclei transcriptomic of Populus tremula x alba apex

Here we applied a novel approach to isolate nuclei from complex plant tissues (https://doi.org/10.1371/journal.pone.0251149), to dissect the transcriptome profiling of the hybrid poplar (Populus tremula × alba) vegetative shoot apex at single-cell resolution. We harvested 20 shoot apices from 3-weeks-old in vitro grown plants and performed high-throughput, microfluidic-based single-nuclei RNA sequencing (snRNA-seq) using the 10× Genomics Chromium technology. For all quality control and analytical steps, we used Asc-Seurat, a comprehensive web application that encapsulates a series of tolls for scRNA-seq data analysis. To annotate each cluster, we assessed the abundance of transcripts of poplar homologous to Arabidopsis well-known cell type marker genes for the different domains of the vegetative or reproductive shoot apex.