Whole leaf vs. Leaf protoplst bulk RNA sequencing dataset

The leaf vasculature plays a key role in solute translocation. Veins consist of at least seven distinct cell types, with specific roles in transport, metabolism, and signaling. Little is known about the vascular cells in leaves, in particular the phloem parenchyma (PP). PP effluxes sucrose into the apoplasm as a basis for phloem loading; yet PP has only been characterized microscopically. Here, we enriched vascular cells from Arabidopsis leaves to generate a single-cell transcriptome atlas of leaf vasculature. We identified ?19 cell clusters, encompassing epidermis, guard cells, hydathodes, mesophyll, and all vascular cell types, and used metabolic pathway analysis to define their roles. Clusters comprising PP cells were enriched for transporters, including SWEET11 and SWEET12 sucrose and UmamiT amino acid efflux carriers. PP development occurs independently from APL, a transcription factor required for phloem differentiation. PP cells have a unique pattern of amino acid metabolism activity distinct from companion cells (CC), explaining differential distribution/metabolism of amino acids in veins. The kinship relation of the vascular clusters is strikingly similar to the vein morphology, except for a clear separation of CC from the other vascular cells including PP. In summary, our scRNA-seq analysis provides a wide range of information into the leaf vasculature and the role and relationship of the leaf cell types. Overall design: mRNA profiles of whole leaf and protoplasts from Col-0 plants grown in short day (8hr light/16hr dark) condition Total RNA was extracted from leaves (not protoplasted) and leaf protoplasts isolated using the same method for the single cell sequencing using the RNeasy Kit. Two biological replicates were made for leaf and leaf protoplast samples. Libraries were constructed using the ULTRA II directional library kit and size selection was done using SPRI beads. QC-tested libraries were sequenced on an Illumina HiSeq 2500 lane with 150 bp paired-end.