Cell type-specific expression atlas of the early Arabidopsis thaliana embryo

The establishement of the first plant tissues occurs during embryo development. Indeed, cell types that will form the Arabidopsis root stem cell niche are first specified during 16-cell (16C), early globular (EG) and late globular (LG) stage of embryonic development. While some regulatory factors are known, we do not yet understand the genetic networks underlying the specification of these cell types. One main reason for this is the difficulties in adapting genome-wide approaches to the cellular level. Here, we have adapted such an approach (INTACT) to generate microarray-based cell type-specific transcriptomic profiles at 16C to LG stage for use in determining the role of the transcriptome in cell specification and differentiation during root stem cell niche formation. We manually pollinated flowers and isolated cell type-specific nuclei from embryos using the INTACT method and cell type-specific markers at 16-cell stage (72h after pollination), EG stage (81h after pollination) and LG (100h after pollination) of development. Following RNA isolation, microarray-based transcriptomic profiling was performed on 3-4 pooled biological replicates each.