Figure 1.

Readout of high complexity shRNA pools. (a) Surface plot of signal intensities for all 248,049 shRNA features on the GMAP microarray following hybridization of probe generated from the human 78 k plasmid shRNA pool or the mouse 78 k plasmid shRNA pool. The surface plot shows the signal intensity distributions of the human and mouse 78 k features plotted against each other and the remaining shRNA probe features not corresponding to either pool. The signal peaks are labelled according to which set of features they represent. (b) Distribution plots of GMAP features data for a dilution series of shRNAs in separate pools. 4x, 16x, and 64x curves are plotted as the distribution of log2 difference between the array signal for shRNAs in the dilution series and their signal in the reference (Even) pool. The 1x curve is plotted as the log2 difference between a group of undiluted shRNAs in the 4x pool and the same shRNAs in the Even pool. (c) Distribution plots of GMAP array data for a dilution series of shRNAs within the same pool. 2x, 5x, 10x, and 20x curves are plotted as the distribution of log2 difference between the array signal for groups of diluted shRNAs and their signal in the reference (Even) pool. The 1x curve is plotted as the log2 difference between a group of undiluted shRNAs in the 2x-20x pool and the same shRNAs in the Even pool. All microarrays were run in triplicate, and the replicate signal intensities were averaged.

Ketela et al. BMC Genomics 2011 12:213   doi:10.1186/1471-2164-12-213
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