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Figure 3 | BMC Genomics

Figure 3

From: Decoding pooled RNAi screens by means of barcode tiling arrays

Figure 3

Barcode tiling probe performance in negative selection RNAi screens. A - Colored squares represent the six tiling probes complementary to each barcode sequence. Black spots represent signal intensity profiles at time point zero from each of the barcode sequences included in the pooled screen. The intersection of the dashed lines marks the position of the centroid. Validated candidate constructs are highlighted. B - Tiling probes with reference (tzero) signal intensities below a 10-fold median background intensity threshold were excluded from analysis. Shown are percentages of 305 shRNA expression constructs included in the pooled screen that were detectable by the indicated number of barcode tiling probe sequences above the 10-fold threshold. For 91 percent of the shRNA expression constructs more than one barcode tiling probe matched those criteria (right of the dashed line). Only those barcodes were considered for further analysis. Percent values represent absolute counts from Additional file 2 relative to the total number of 305 shRNA expression constructs. C - A heat map was generated from log2 ratios obtained from each tiling probe (TP) that passed the filter criteria, corresponding to log2 values in Additional file 2. Columns represent the six different tiling probes and lines the 278 barcode sequences retained after filtering sorted by their tiling probe mean log2 values. White cells represent tiling probes which did not pass the described filter criteria.

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