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Since there was not an already defined clustering (except for the time point indicators), we optimised the threshold by maximising the average silhouette value, as it was done for the PAM algorithm [14].
For each time point at least four hybridizations were carried out corresponding to 3 biological replicates and one dye-swap, except for the time point corresponding to 24 h of culture.
Four hybridizations were carried out per time point to obtain the expression value for each gene (fold change of normalized signals), except for the time point corresponding to 24 h.
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The dendrogram obtained (data not shown, but equivalent to the sample clustering in Figure 1) gave the same sample classification as the nuclear morphology, except for the time points DEV2 and DEV3, which could not be resolved.
As shown in Figure 3(a), SCAPs in activator group exhibited higher proliferation, while the SCAPs-inhibitor group showed less proliferation capacity as compared with the corresponding control groups, respectively (P < 0.05), except for the time points at baseline (day 0) and the first day.
Except for data recorded at the time point of intubation, all data were normally distributed.
BPA exposure significantly impacted IGF-1Ra transcript levels with significant down-regulation observed in embryos reared from oocytes exposed to the higher BPA treatment for all the time points except 13-dpf (Fig. 6C).
In order to impute missing data, we first calculated the full samples' mean cortisol change between the time point with the missing value and the adjacent time point; for all time points except awakening, we used the time point prior to the missing value.
The behavior of GAL4, which is expected to switch off, shows no expression at all times in our predicted model, therefore predicting the time series except for the initial time point.
We therefore do not see the data as directly comparable except for the initial time point.
Blood was collected 20 days after the first immunization and 14 days after subsequent immunizations for analysis by ELISA (all collected via retro-orbital bleed except for the final time point, which was by cardiac puncture).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com