Time-series of the seed-to-seedling transition in Arabidopsis thaliana

The expression levels of Arabidopsis thaliana (Col-0) genes in several developmental stages during the seed-to-seedling transition were measured by using high-density Affymetrix® arrays (Aragene.st1.1). We used a time-series of microarrays to gain temporal resolution and identify relevant genes in the seed-to-seedling transition. To elucidate the changes in the transcriptome related to the transition from a seed to a photo-autotrophic seedling, seven developmental stages were defined: (DS) mature dry seed; (6h) seeds, imbibed for 6h and germination-related initiation of metabolic activity; (TR), embryo swelling and testa rupture; (RP) protrusion of the radicle through the endosperm, primarily through cell elongation, followed by further embryonic root extension and beginning of (RH) root hair formation, succeed by the appearance of (GC) greening cotyledons and (OC) cotyledons that are fully opened. Three biological replicates represented by pools of seeds bulk-harvested from three to four plants were used.