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In the second step, we filtered putative whi or lge gene deletions according to the total number of times a replicate for either barcode tag was detected above the array-specific Z score thresholds.
Then, in order to remove possible problems of interpretation due to pseudoreplication, we employed a randomization procedure that consisted of selecting at random one individual from each Petri dish and averaging the response (cannibalistic "1" or non-cannibalistic "0") across mothers, using each mother as a replicate, for analysis with the Mann-Whitney U-test.
A replicate for each fungal strain consisted of ten individual flasks, and one of each was used once every day for sampling.
Three plots of each variety were grown using a randomised block design; each plot served as a replicate for all subsequent analyses.
Throughout all experiments, each fish was treated as a replicate for both aromatase activity and cyp19b expression (n = 6) because space for individual experimental units was limited.
For the analysis of life span, total number of eggs and number of neonates each individual female was a replicate; for the hatching proportion, we used the proportion of the whole cohort as input variable.
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Within a biological replicate, for a tissue sample, the same cDNA pool was used for qPCR analysis of each of the nine genes using gene-specific primers.
This is illustrated in Figure 5, which presents the Manhattan plots of SNP effects on a random replicate for a medium-density chip and whole-genome sequence data.
A replicate spot for which either channel was flagged as poor quality was excluded from these calculations.
One group had performed a replication analysis for their samples (GDS2106), which we used here as a fourth comparator being a technical replicate for the observations in GDS2106.
Additionally, a small aliquot of each experimental sample was pooled together to serve as a technical replicate for duration of the run.
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