Isolation of living apical and basal cell lineages of early proembryos for transcriptome analysis

Plant zygotes usually undergo asymmetrical cell division, giving rise to the formation of two daughter cells with distinct developmental cell fate. The small apical cell will develop into the major part of embryo proper, whereas the larger basal cell will divide to form a transient suspensor. Thus, the apical and basal cell lineages are an excellent model to study cell fate determination in relation to zygote polarity. However, the molecular mechanism underlying the differentiation of two distinct cell lineages is not yet understood, possibly due to the technique limitations. Previously, we have established a protocol for isolating apical cell and basal cell for cDNA library construction in tobacco. However, the method for isolating tiny Arabidopsis embryos has long been considered much more difficult. Here, we present a detailed protocol for isolating early Arabidopsis proembryos and separating apical and basal cell lineages of proembryos, which allow us to establish cell lineage-specific transcriptomes of early proembryos.