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The cell line demonstrated a highly comparable behaviour in each batch (data not shown).
All repeats clustered next to the first sample run irrespective of the differences in print batch (data not shown), hence replicate assays were merged in a weighted fashion, as previously described [ 58].
We had also recently shown that commercially available carboxylated PLG nanoparticles coupled with peptides could induce immune tolerance, but the tolerogenic efficiency was highly variable based on batch (data not shown).
However, the absence of CNAs detected in five cases having no or very few tumor cells as well as the absence of CNAs detected in normal samples analyzed in the same batch (data not shown) support the good specificity of our method.
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Induced expression level of some of the starvation markers during the lactose (fed-batch, data not shown) or medium feed (acs1, continuous culture, Figure 6C) further indicated that too little substrate was available for the culture at this low dilution rate.
However, gene expressions in most other ecotypes were not consistently high or low among batches (data not shown).
The reproducibility of the antigen preparation method was confirmed by the comparison of three separately manufactured batches (data not shown).
The two-fold criterion was imposed because all FFPE assay measurements were reproducible within a two-fold window (approximately 20% coefficient of variation); [ 39]), both within a single batch and between multiple independent batches (data not shown).
As the samples were hybridised in two rounds on two different array print batches and initial clustering of the samples indicated batch effects (data not shown), the data were adjusted to minimise this effect.
Control experiments in batch culture (data not shown) have indicated that, following the ammonium impulse, phosphate (not sulphate or glucose) would become the growth-limiting nutrient.
In the current study a parameter value of 0.66 h-1 was estimated from the growth kinetics of E. coli LE392 cells cultivated in minimal (M9) medium supplemented with glucose in a batch reactor (data not shown).
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