Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots

We performed a time course analysis (TC data set) of the response of whole seedling roots to -Fe at 6 time points after transfer (3, 6, 12, 24, 48, and 72 hours). Little is known about how developmental cues affect the way cells interpret their environment. Here we characterize the transcriptional response of different cell layers and developmental stages of the Arabidopsis root to high salinity and find that transcriptional responses are highly constrained by developmental parameters. These transcriptional changes lead to the differential regulation of specific biological functions in subsets of cell-layers, several of which correspond to observable physiological changes. We show that known stress pathways primarily control semi-ubiquitous responses and use mutants that disrupt epidermal patterning to reveal cell-layer specific and inter-cell-layer effects. By performing a similar analysis using iron-deprivation we identify common cell-type specific stress responses and environment-independent biological functions that define each cell type. Keywords: time course analysis Seedlings were grown for 5 days before transfer to iron deficient (-Fe) conditions (0.3mM Ferrozine in MS media containing no iron sulfate). Whole roots were harvested at 6 time points after the transfer.