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Figure 4 AFM images and C - AFM current map for samples annealed without a protective carbon capping layer.
Figure 3 AFM images and C-AFM current map for samples annealed with a protective carbon capping layer.
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The elemental distribution map for sample 2 was collected in the same manner as sample 1, except the beam size was 10 × 10 μm and step size was 7 μm.
AR FISH maps for samples 3 and 4 are shown in Figure 4A and B. For sample 4, we detected small regions (foci) of cells with Cat5 and Cat4 alterations: both of these foci had been selected in the TMA cores (Table 3).
Details on read mapping for sample FD1.
Details on read mapping for sample DTT1.
Details on read mapping for sample CsCl1.
We obtained 314.2 million raw reads on a single lane, after barcode mapping for sample allocation we obtained 65.2 million reads for RNA-seq sample 1 and 58.8 million reads for RNA-seq sample 2 respectively.
The computer software program FlapJack [ 49] was used for graphical genotyping and visualization of the genetic map for all samples and to indicate the positions of SNP markers with known chromosome locations.
These membership weights (W rj ; range from 0 to 1, with 1 indicating an unequivocal prediction of the conclusion C r ) were visualized in a heat map for all samples (j) and all rules.
This process was repeated for eight iterations, yielding a high quality consensus optical map for that sample.
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