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Using this approach, 735 unique tyrosine phosphorylation sites in the two biological replicates were identified.
Differential peaks between samples with two biological replicates were identified by diffReps.
Secondly, DE genes between Cy3-labelled nonconfluent and confluent samples (biological replicates) were identified using the same approach.
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Each biological replicate was identified by a different index.
Using the same software, all three biological replicates were overlaid to identify repetitive CNV events.
Data from three biological replicates were combined, and we identified 488 p73 sites at a significance threshold of P≤10−5, the same cut-off used for the p63 analysis previously described [24].
For each genotype, signal intensities from three independent biological replicates were averaged and genes identified that were differentially expressed in the edm2 or wnk8 mutants compared to either Col-0 or pXVE:HA-EDM2-a (see methods).
Only proteins which were identified in at least two biological replicates were considered.
Two or three biological replicates were used in each stage to identify transcripts that showed significant differences at a FDR cutoff < 0.05 between developmental stages (E9.5, E11.5 and E13.5) by Cuffdiff v1.2.1.
Cy3/Cy5 ratios of the 3 biological replicates were averaged and then used to identify modulated genes using 1 Way-ANOVA with a cut-off of 1.5-fold change and a Student's t-test p-value of less than 0.05.
Only proteins identified in both biological replicates were considered and combined for analysis.
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