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Initially LC3 spots were counted by creating a spot mask on CD8+ cells positive for LC3, spot to background ratio was set to 2.25 and the radii of spots was set as 1, γH2AX spots were counted in a similar way with spot to background ratio set at 5. These spot masks were then converted into a feature and were used to plot against normalized frequency of cells.
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We use the parameter settings of the HKY model employed in MONKEY (Moses et al., 2004, 2006), so that the transition transversion ratio is set to 3.8, and the background distribution, B, is set to BA= BT=0.3 and BC= BG=0.2.
At the moment, that ratio is set at 3%.
Ratios are set according to driving conditions, rather than in the distinct steps of conventional transmissions.
Genomic coordinates for protein-coding transcripts were obtained from Xu et al. [ 14]. Background signal was set to 1.2 standard deviations above the mean of the ChIP:input ratios and then subtracted from the ChIP-seq signal.
The background density was set to 0 g/cm3.
A background ROI was set adjacent to the left ventricle.
The background threshold was set at twice the background fluorescent signal plus 3 standard deviations.
The background correction was set to: offset = 50.
Signal-to-noise ratio (SNR), that is, signal/standard deviation of background, was set as the final signal of each protein.
Background white noise was set at 70 dB.
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