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The mean RPKM of three biological replicates was compared among different samples.
Next, the reproducibility between biological replicates was compared among MICC, ChIA-PET tool and ChiaSig.
To select differentially expressed genes, the average of two biological replicates was compared between the conditions examined.
Samples compared are described in row 1 (eg. "OV_vs_TE") Mean read intensity (from two biological replicates) was compared between samples using DESeq and adjusted p-value (padj).
For sporulation assays determined with the microscopic method, the mean percent sporulation in the presence of antibiotic from 3 biological replicates was compared with the corresponding control without antibiotic.
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The averages of biological replicates were compared for the different strains and summarized as pie charts (Fig. 2 a).
The three biological replicates were compared.
Expression levels obtained from four independent biological replicates were compared using FlexArray 1.1 software [ 15].
The observed technical reproducibility is very high and variability may be higher when two biological replicates are compared.
Upon meeting these criteria the independent biological replicates were compared, resolving 1016 SARs and 775 MARs along chromosome 16.
Four biological replicates were compared: in all four the normoxic samples were labeled with Cy3 and the hypoxic samples were labeled with Cy5.
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