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For most samples, we perform multiple stages of laser annealing and characterization, with laser power increased between each stage.
In order to investigate the interface asymmetry of the four samples, we perform RDS measurements at 77 K and the results are shown in Fig. 5.
Due to the high number of features and the limited number of samples (i.e. 870 samples), we perform a feature selection step.
In order to investigate the interface asymmetry of the four samples, we perform RDS measurements at 77 K. RDS can precisely measure the reflectance difference between [110] and [1(bar {1} 0] directions, i.e., (Delta r/r=2(r_{110}-r_{1bar {1}0})/(r_{110}+r_{1bar {1}0})), resulted from interface asymmetry of the QWs.
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To estimate algorithm performance on novel samples, we performed leave-one-out cross-validation (LOOCV), in which the top-scoring pair as determined by N-1 samples is used to predict the left-out sample class.
For the HD samples, we performed a small-pool PCR as described in37 (Supplementary Fig. S7).
To further identify genome-wide H3.3 distribution changes after DAXX inhibition in PTEN-null/GBM-PDX samples, we performed unbiased chromatin immunoprecipitation sequencing (ChIP-seq) (Supplementary Fig. 9a).
Due to the strong cytoplasmic signal observed by immunostaining in the angiosarcoma samples, we performed a western blot on tissue sections from an angiosarcoma patient and confirmed that two bands could be detected by western blotting analysis, with the lower band matching the molecular weight reported for Myc-nick (Supplementary Fig. 7b).
Because of the predefined number of available biobank samples, we performed post hoc power calculations and included confidence intervals for MAF differences (according to [19]) (Additional file 1: Figure S1 and Table 1).
Results were expressed as area under the curve (AUC) of luminescence during the 20 min. For some samples, we performed several measurements to test reproducibility of the luminometric analysis under different conditions that might be encountered in clinical practice.
In addition to the comparison between the entire Argentinian and North American samples, we performed a more specific comparison between only the subgroups with early onset, defined as occurring at less than or equal to 21 years of age.
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