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Non-specific binding to the reference anti-human Fc surface was not observed.
The data was processed by subtracting background binding to the reference flow channels (FC1 & FC3).
In fact significant negative responses were obtained after subtracting responses from the reference flow cell due to binding to the reference.
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The copurified RNA fragments are amplified and sequenced and mapped back to the reference genome to reveal RBP binding sites.
This linear relation can be derived from the ratio of the specific binding to the nondisplaceable binding using different reference regions (see Appendix).
Comparisons of the binding site to the reference structure, here FLT3, can be displayed, along with root-mean-square deviation values, in this case indicating that the binding sites of these protein kinases are highly conserved.
Requiring that peptides in the non-ligand data set were found both with stronger and weaker binding affinities compared to the reference ligand further reduced the set of ligand:non-ligand binder pairs to 459.
No binding was observed to the reference channel.
Protein-DNA binding can be skewed to the reference allele (SR), skewed to the non-reference allele (SN), or not allele-specific (NS).
In order to show Pyicos applicability to CLIP-Seq experiments, we reproduced the results from Xue et al. (2009), where the interacting RNA sites for the polypyrimidine tract binding protein were mapped to the reference human genome.
Curves for binding to a blank reference chip were subtracted using the software package Biaevaluation (GE Healthcare).
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