Expression data from Col-0 and mcu123 roots of 20-d-old seedlings grown in a sterile hydroponic system.

Ca2+ signaling is central to plant development, modulating gene expression to enable highly specific plant responses. While Ca2+-responsive proteins have been investigated intensely in plants, only few Ca2+ channels are known, and our understanding of how intracellular Ca2+ fluxes are facilitated remains limited. We obtained an Arabidopsis triple knockout mutant of homologues of the mammalian mitochondrial Ca2+ channel-forming MCU protein, in which mitochondrial Ca2+ uptake was severly perturbed in vivo in roots. To pinpoint the impact of the distrupted mitochondrial matrix free Ca2+ dynamcis, we performed transcriptome analysis in roots of an MCU triple knockout background (mcu123) and its corresponding wild type background (Col-0). We devised a microarray-based analysis to investigate transcriptome differences in roots of mcu123 triple knockout backgroudn and Col-0, without additional stimulation, and idenfitied distinct classes of differentially abundant transcripts. Two genetic backgrounds (Col-0 and mcu123) were used for RNA extraction in five replicates and hybridization of Affymetrix microarrays. Each replicate consists of pooled roots of 20-d-old seedlings grown in sterile hydroponics boxes (Phytatray II; Sigma-Aldrich, Darmstadt, Germany) filled with 150 mL half-strength Murashige and Skoog (MS) medium supplemented with 0.1% (w/v) sucrose and 0.05% (w/v) MES, pH 5.8 (KOH).