As cluster analysis was the major goal of this study the microarray experiment followed a reference design, where all samples were hybridized against a common reference sample.
To examine whether a combination of microRNA prediction databases would outperform any one source, data from 15 publicly available microRNA over-expression/knockdown experiments followed by microarray [53], [54], [55], [56], [57], [58], [59], [60], [61] was assembled (Table 3).
Chromatin immunoprecipitation experiments, followed by intergenic microarray or quantitative PCR analyses, were performed as previously described [ 2].
QRT-PCR was used to validate selected data from the microarray experiments and to follow the expression of a subset of genes over time.
The microarray-based MIP preparation and capture experiment followed MIP standard-operating procedures with modifications in the preparation of probes (manuscript in preparation) [ 17].
The minimum information about microarray experiments (MIAME) guidelines were followed for all microarray experiments conducted in this study [ 36].
The guidelines described in MIAME (Minimal Information About a Microarray Experiment) has been followed in writing this paper.
The array data is deposited at Gene Expression Omnibus (GEO), (http://www.ncbi.nlm.nih.gov/geo) and the MIAME (minimal information about a microarray experiment) guidelines was followed for data presentation.
In planning the microarray experiments, we chose to follow a cyclic design according to which we compared, for example, WT-vitro to AP-vitro, then AP-vitro to AP-vivo, then AP-vivo to WT-vivo, and then WT-vivo to WT-vitro (Fig. 1).
