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The sets of validated peak lists are provided to the external programs that determine torsion angle restraints, assign NOESY peaks, calculate structures and analyze secondary structure.
Based on an analogous de novo motif discovery performed on the sub-sequences of validated peak regions taken from the promoter regions of the 33 core OCT4 target genes only, a motif similar to the binding site of E2F was obtained (consensus sequence GSmkGs) and could be mapped to the promoter regions of ORC1L and further OCT4 target genes (data not shown).
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To validate peak assignments of the Tyr isomers, co-chromatography was performed with synthetic m-Tyr or o-Tyr added to proteome samples.
Pure standards for vanillin, vanillic acid, acetovanillone, syringaldehyde, syringic acid, acetosyringone, and p-hydroxybenzoate (Sigma-Aldrich, St . Louis MO, USA) were used to validate peak compound identification and for quantitation.
Searching for instances of conserved TF binding motifs at the predicted binding loci is considered the most prominent verification method for validating peaks [ 14].
The results are validated using peak signal to noise ratio and structural similarity index measures.
As shown in Figure 4D & E, all but one of the 20 top peaks validated as did 80% of the peaks from the middle or bottom ranked lists.
We validate our peak topographic methods across a set of 34 (GCtimes GC) injections from a diverse portfolio of petroleum sources, including a wide range of samples collected from the MW, the source of the Deepwater Horizon disaster in the Gulf of Mexico, April 2010.
To validate this peak set, randomly selected targets were tested in ChIP-qPCR using three new biological ChIP samples (Figure 3B).
To do so, we first identified sites that might be unique to fer-1 or fer-1 ; him-8 using MACS2.1 (see the section Materials and Methods), and then visually inspected all sites that had been called as unique to one genotype to validate the peak calling.
To validate the peak intensity on the SELDI-TOF-MS protein profile with absolute concentrations determined by routine method, the SAA concentration was measured by an immunoassay kit in samples of both the lung cancer sera (n=38) and the healthy control sera (n=34).
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