A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies

Whole-genome transcriptional profiles of rice cell types, isolated by laser-capture microdissection. The first comprehensive multi-organ cell type transcriptome atlas from a plant, with 40 distinct cell types from several developmental stages of seeds, shoots and roots, reveals cell-specific promoter motifs, interaction partner candidates, hormone response centers, and other previously unrecognized cellular properties and patterns. Keywords: Cell type comparison For GSM329492-GSM329659: Microarray experiments for 40 cell types and two organs were organized using a common reference statistical design, to assure data for all cells could be normalized for cross-comparison. In this design, the hybridization for each cell type sample included a second probe made from an RNA sample that served as a Common Reference, identically aliquoted from a single preparation, for all hybridizations, and including dye swaps for the two probe labels. The Common Reference RNA for all hybridizations was prepared from rice suspension cultures, selected as an undifferentiated cell type that expresses a relatively high percentage of its genome. Although this is an abundant source of RNA, the Common Reference RNA was amplified and labeled in identical fashion to other probes. At least four independent biological replicates for each cell type were collected and profiled; only microarray data sets with r >= 0.9 were retained. A dye swap was included, in which each cell type sample and the Common Reference were labeled with Cy3 and Cy5, respectively, on the two replicates and the reverse for two replicates. For GSM588319-GSM588370: We analyzed 4 replicates for each cell type and compared with cultured cells. Each replicate contains 2 slides.