Microarray data

have been submitted to ArrayExpress under accession number A-MEXP-1990. Total RNA was purified using the RNeasy Mini Kit (Qiagen, Hilden, Germany). Cells were disrupted in RLT buffer provided with the Kit in Fast Protein tubes (Qbiogene, Carlsbad, CA) using the Ribolyser (Hybaid, Heidelberg, Germany) (30 s, level 6.5) before spin column purification according to the RNeasy Mini Kit RNA purification protocol. Fluorescent-labeled amplified RNA was prepared using the MessageAmp II-Bacteria RNA Amplification Kit (Applied Biosystems, Darmstadt, Galunisertib Germany). Starting from 500 ng total RNA, cDNA carrying a terminal T7 promoter was synthesized. Subsequent in vitro transcription resulted in aminoallyl-modified RNA that was labeled ABT-737 manufacturer with Cy3- or Cy5-N-hydroxysuccinimidyl ester dyes (GE Healthcare, Little Chalfont, UK). Uncoupled dye was removed applying the RNeasy MinElute Kit (Qiagen). Processing of microarrays before hybridization included the following washes: once in 0.1% Triton-X100 (5 min, 20 °C); twice in 0.032% (w/v) HCl (2 min, 20 °C); once in 0.1 M KCl (10 min, 20 °C); once in H2O (1 min, 20 °C); once in 0.064% (w/v) HCl,

1 × Nexterion blocking solution (Schott AG) (15 min, 50 °C); and once in H2O (1 min, 20 °C). Microarrays were dried by centrifugation (3 min, 185 g, 20 °C). Hybridization was performed in an EasyHyb hybridization solution (Roche, Mannheim, Germany) supplemented with sonicated salmon sperm DNA at 50 μg mL−1 in a final volume of 100 μL for 90 min at 45 °C much using the HS 4800 hybridization station (Tecan Trading AG, Switzerland). Before application to the microarrays, labeled samples were denatured

for 5 min at 65 °C. After hybridization microarrays were washed once in 2 × SSC, 0.2% sodium dodecyl sulfate (SDS) (w/v) (5 min, 42 °C), twice in 0.2 × SSC, 0.1% SDS (w/v) (1 min, 21 °C), twice in 0.2 × SSC (1 min, 21 °C), and once in 0.05 × SSC (1 min, 21 °C). Following the washes, slides were dried by centrifugation (3 min, 185 g, 20 °C) and scanned with a pixel size of 10 μm using the LS Reloaded microarray scanner (Tecan Trading AG). Four independent biological replicates including a dye swap were processed for each comparison. The mean signal and the mean background intensities were obtained for each spot of the microarray images using the imagene software 6.0 software (Biodiscovery Inc., Los Angeles) for spot detection, image segmentation, and signal quantification. Spots were flagged as ‘empty’ if R≤0.5 in both channels, where R=(signal mean−background mean)/background SD. The remaining spots were considered for further analysis. After subtractions of the local background intensities from the signal intensities and the introduction of a floor value of 20, the log2 value of the ratio of intensities was calculated for each spot using the formula Mi=log2(Ri/Gi).