Root cell-type-specific transcriptome of SCR root cells with the treatment: WCS
Whole root tissue for the unsorted control was lysed by grinding with a liquid-nitrogen-cooled mortar and pestle. RNA was isolated with the RNeasy Plant Mini Kit (Qiagen) for the six unsorted whole root samples and for six out of eight sorted whole root samples. RNA from the remaining two sorted whole root samples and all cell type-enriched samples were isolated with the Micro Kit (Qiagen). RNA concentration was checked with a Qubit Fluorometer (Thermo Scientific) and RNA integrity was assessed with a Bioanalyzer (Agilent Technologies). Subsequently, RNA libraries were made from samples with RNA integrity number (RIN) values above six. All libraries were made with the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB). RNA for the six control unsorted (whole root) and the first six control sorted samples were poly-A selected using Dynal Oligo-dT beads. These twelve libraries were generated using 100 ng of total RNA. The remaining libraries were generated from total RNA selected using NEBNext Oligo-dT beads. Because of limited RNA yields from some of the sorted cell populations, 50 ng of total RNA was used as starting material for all sorted library preparations. Libraries were sequenced on an Illumina HiSeq 2500 using 50 base pair Single-Read (Duke University Sequencing Core).