High-throughput single cell transcriptome profiling of plant tissue

Plant tissues are composed of diverse cell populations, but their individual transcriptional profiles are not well characterized. High-throughput single cell RNA sequencing technologies can deconvolute heterogeneous tissues but have not been adopted for plants. Exploiting Arabidopsis root protoplasts as a model, we used Drop-seq to profile >4,000 individual plant cells, capturing a diversity of cell types, identifying novel marker genes, and illuminating developmental trajectories of endodermis and hair cells. Two technical replicates of scRNA-seq data as well as whole tissue RNAseq from 5-day-old Arabidopsis roots were generated using Illumina HiSeq4000