Identification of auxin and cytokinin cross-talk components involved in lateral root initiation

Genome wide transcriptome profiling of pericycle cells from roots exposed to auxin, cytokinin and both hormones simultaneously. Lateral root organogenesis in Arabidopsis is governed by a complex network of hormonal regulations. Plant hormones auxin and cytokinin were demonstrated to be the key regulators of this lateral root organogenesis and their mode of interaction is antagonistic. The aim of the project is to understand the role of the auxin - cytokinin signalling pathways in lateral root organogenesis. 12 samples (4 conditions with 3 replicates for each). J0121 seedlings were growing on MS. These 5 day-old seedlings were used for different treatments: 1µM NAA 3h (NAA); 10µM BAP 3h (BAP); 1µM NAA + 10µM BAP 3h (NB). After cell sorting the RNA were extracted from pericycle cell sorted using the RNeasy Plant Mini Kit (Qiagen). A DNase treatment with the RNase-free DNase Set (Qiagen) was carried out for 15 min at 25°C. Total RNA concentration was determined using a Nanodrop ND-1000 spectrophotometer. All RNA samples were rejected if they did not reach a minimum concentration of 100 ng μl−1, a 260 nm/280 nm ratio between 1.8 and 2.0 and a RNA integrity number superior to 7.5, measured with an Agilent 2100 Bioanalyzer (Agilent, USA). Arabidopsis Tiling 1.0R arrays (Affymetrix) were hybridized at the VIB Nucleomics Core (www.nucleomics.be) according to the manufacturer’s instructions. Data were normalized from CEL files using the robust multiarray average (RMA) algorithm (Irizarry et al., 2003). The probe annotation was obtained from athtiling1.0rcdf (Naouar et al., 2009). Differential expression analysis was determined using the eBayes function from the limma package in R (Smyth, 2004). P values were calculated and then transformed into false-discovery rates (FDR), or Q values according to the method described by Storey and Tibshirani (2003), as implemented in the R package qvalue. Please note that the Data.xlsx contains the result from differential expression analysis (and the full set of normalized data for each individual sample is not available).