Image acquisition, data processing, and analysis of PBM11

Two different images were obtained for each microarray at 5 μm in a GenePix 4000B scanner (Axon Instruments) and quantified in the GenePix Pro 5.1 software. One corresponded to double-stranded DNA at 635 nm, generating “control DNA” GPR files. The second image was obtained after labeling of DNA-protein complexes at 532 nm, generating “binding” GPR files. Combining of “control” and “binding” files, normalization and adjustment of the probe intensities and transformation to a list of scores for all the k-mers considered were carried out with the PBM Analysis Suite from Berger and Bulyk (2009); http://the_brain.bwh.harvard.edu/PBMAnalysisSuite/index.html. We adapted these scripts to the dimensions of our PBM11 microarray and for calculating average intensities of duplicated probes. The best scored motif, represented as an energy- based matrix, was converted into a graphical logo with the on-line tool enoLOGOS (http://chianti.ucsd.edu/cgi-bin/enologos/enologos.cgi).