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As expected, silencing of USP7 resulted in PML stabilization in both replicates in the absence of arsenic trioxide (Figure 6A, compare lanes 1 and 3 with lanes 2 and 4).
Of these, 22 noncontaminant proteins significantly differed (P ≤ 0.05) in both replicates in the same trend (Supplementary Materials (Table S2)).
For the HT-1080 experiments, only genes with FPKM not equal to zero in any condition and FPKM ≥1 for both replicates in the DMSO-treated condition were considered in the analysis.
Again, Pearson correlation tests were performed separately for each origin, and both replicates in the hatchery control treatment were compared to the two replicates in the restricted hatchery treatment.
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Also of note are the two SNPs rs8094327 and rs12606138 within NEDD4L that both replicated in the case-control samples.
At the minimum read threshold of 2, a fusion was either detected or not detected in both replicates in 93% of the cases.
Only when the signal is statistically significant (p-value < 0.5) in both biological replicates in the window, we report the region as a significant DIR.
The way we incorporated the reproducibility in our study was to consider only signals as relevant that reached a certain threshold in both replicates, as was the case in the analysis by Wade and colleagues.
As the parasite inhabits both extracellular and intracellular niches and replicates in the mosquito vector and mammalian host, its ability to scavenge host nutrients to support replication presumably varies greatly depending on its environment.
The indicated peak at 97C was greater than all permutation values and was observed in both replicates, as was the peak near the tip of the X-chromosome in the vicinity of yw.
We used GATK to call SNPs across the strain panel, focusing on SNPs identified in both replicates of the genomic DNA sequencing (for the replicated data in the strain panels).
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