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The total energy with each CWSS method is normalized.
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The fold-change values of identified 372 proteins (Additional file 1) by using the Reporter Ions Quantifier with the TMT 6-plex method were normalized using global median.
A crossing point (CP) determined for each gene of interest, using a Second Derivative Maximum Method, was normalized to the mean CP for Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in the same sample.
The results obtained using the fluorescence method were normalized per cell autofluorescence level, which could be related to the presence and senescence-associated increase in the lipofuscin content (Ksiazek et al. 2009b).
In the second method, the temporal CSD is normalized by the ensemble averaged PSDs.
Finally, in the third method, the smoothed CSD is normalized by the ensemble averaged PSDs.
For the ratio system of the MOORA method, first, the decision matrix is normalized using Eq. (2) as seen in Table 4.
Using this method, the number of reads is normalized with respect to the sequencing depth and the length of a given gene.
While in the UpQu normalization method, counts are normalized by division (in a given replicate) by the upper quartile of these counts, the Medi simply computes the median, and the ToCo uses the sum of all counts.
Data were analyzed using Ct method and were normalized by RNU6B expression.
qRT-PCR was performed with the SuperScript® III Platinum® SYBR® Green One-Step qPCR Kit w/ROX (Invitrogen) and data was analyzed with 7500 Real-Time PCR System software (Applied Biosystems) using the 2−ΔCT method, data were normalized to β-actin1 for zebrafish and ACTB for fibroblasts.
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