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In microarrays experiments, a serious limitation is the unreliability of low signal intensities data and the lack of reproducibility for the resulting ratios between samples and controls.
The change in absorbance between samples and controls was reported as change in absorbance/min/mg protein.
The purpose of this test is to determine whether there is a significant difference between samples and controls, while taking into account issues of reaction efficiency and reference gene normalization.
Concerning assessment of expression of Has genes, the endogenous control Gapdh, used in real-time PCR analysis to normalize for differences in the amount of total RNA added, were in some cell/growth factor combinations not at a consistent level between samples and controls.
Selection of differentially methylated CpGs or unmethylated CpGs was based on the presence of a Delta ß value of at least 0.34 between samples and controls [Δß = samples mean ß value – controls mean ß value] and a false discovery rate (FDR) below 0.05, calculated using t tests or analysis of variance if more than two groups were compared.
The cytotoxicity was obtained by comparing the absorbance between samples and controls.
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Difference between samples and control were evaluated using GraphPad Prism 5.0 software (GraphPad Software Inc., USA).
Competitive hybridizations were carried out on oligonucleotide arrays; processing of the expression data generated ratio intensities between samples and control, with positive values corresponding to genes more expressed in myofibers.
The ΔΔCt method was used to compare relative fold changes between samples and control.
We narrowed down our analysis to four cases that showed significant repression of the targeted gene and performed differential expression analysis between samples and control gRNA using DESeq.
In addition, RE digestion and bisulfite conversion are sources of variability as the initial treatment of DNA can cause non-specific template degradation and confound the relative comparison between samples and control 100% methylated DNA [ 39].
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between patients and controls
between samples and duplicates
between samples and clusters
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between cases and controls
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