Figure 2.

Comparison of sequencing and GMAP performance with high complexity shRNA pools. (a) Scatter plot of GMAP array signal intensity (X-axis) versus sequencing read number (Y-axis) for shRNA clones from the human Even shRNA pool. (b) Distribution plots of Illumina sequencing 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 number of sequencing reads for shRNAs in the dilution series and their read count 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 Illumina sequencing 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 number of sequencing reads for groups of diluted shRNAs and their read count 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. (d) Distribution plots of GMAP features data for a dilution series of shRNAs contained within sub fractions of a ~90,000 shRNA pool where the probe was amplified from shRNA plasmid template DNA. (e) Distribution plots of GMAP features data for a dilution series of shRNAs contained within sub fractions of a ~90,000 shRNA pool where the probe was amplified from genomic DNA of A549 cells infected with lentiviral pools. 2x, 5x, 10x, and 20x curves are plotted as the distribution of log2 difference between the array signal for groups of diluted shRNAs in the 90 k Dilution pool and their signal in the 90 k Reference pool. The 1x curve is plotted as the log2 difference between a group of undiluted shRNAs in the 90 k Dilution pool and the same shRNAs in the 90 k Reference pool.

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