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Three biological replicates were assessed per reaction, each with two technical replicates (using the same sample).
As for the microarrays, cells were purified from 10 males per biological replicate and a minimum of 3 biological replicates were assessed per experiment.
For each experiment, three biological replicates were assessed.
All treatments were performed at 22°C and three independent biological replicates were assessed.
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Reproducibility between the two biological replicates was assessed using Pearson correlation and correlation significance (t conversion).
The microarray data was normalized by median scaling and the quality of the biological replicates was assessed by means of Pearson's coefficient.
The fold change cut-offs selected were necessarily lower than for the transcriptomics approach due to iTRAQ ratio compression, hence their impact on false discovery rates across biological replicates was assessed and found to be low for all runs [Additional file 2].
For quantitative PCR (qPCR), RNA used for mRNA-seq and a second independent biological replicate were assessed.
Each biological replicate was assessed in three technical replicates.
Bovine primary fibroblasts were infected with either SBV, SBVdelNSs or mock-infected and RNA was extracted at 16 h p.i.. Three biological replicates were assesses for each sample and cells were also infected in parallel for immunofluorescence and Western blot in order to confirm that the bovine primary cells were infected by SBV and SBVdelNSs at 16 h.
Three biological replicates and three technical replicates were assessed for gene expression for each of the treatment × genotype × time point × gene groups.
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