Nuclear and cellular expression data from the whole 16-cell stage Arabidopsis thaliana embryo. Arabidopsis thaliana

Due to its inaccessibility, transgenic methods have been recently developed to isolate tissue- or cell-specific nuclear RNA from the Arabidopsis embryo for transcriptomic profiling. While these approaches have made the it possible to conduct transcriptomic studies at the cellular level, only nuclear and not whole celluar RNA can be isolated. The question thus arrises if nuclear RNA is a reasonable proxy for whole cellular mRNA. To answer this, microarray-based transcriptomic profiling was used to determine genome-wide expression in nuclei and cells isolated from whole 16-cell stage Arabidopsis embryos. Overall design: We manually pollinated flowers and either isolated whole embryos (manually using an micromanipulator; cEMB) or the nuclei from embryos (using the INTACT method and a whole embryo marker; nEMB) at 16-cell stage (16C) of development (72h after pollination). Following RNA isolation, microarray-based transcriptomic profiling was performed on 3 biological replicates each.