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Primers shown in Supplementary file 1E were used in ChIP-PCR and qPCR to detect the binding and enrichment of KlF4 regulatory regions after ChIP.
This is because of the limited amount of target antigen present in the mixture, the background binding, and enrichment of phage antibodies specific for non-relevance antigens [ 10].
Here, the vg PRE was able to repress the mw reporter, but not as strongly as at site 3, which is located in 'blue' chromatin, characterized by PcG protein binding and enrichment of the repressive chromatin marker H3K27me3.
We have recently described a peptidomic strategy based on mesoporous silica beads (MSBs) and MALDI-TOF-MS for selective binding and enrichment of plasma low-molecular-weight proteins (LMWP) [ 29], which has been extended also to IS [ 18].
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The sequence-based TF binding related genetic features comprise individual TF binding and the enrichment of modular combinations of TF binding.
We then used a set of Dex/LPS-regulated genes to analyze the distribution and enrichment of binding sites for TFs that were present in Chip-Enrichment Analysis (ChEA) database [ 35].
Despite use of this relatively heterogeneous dataset, we were still able to detect a correlation between strong ALKBH3 binding at group I promoters and enrichment of factors involved in gene activation.
The isolation of surrogates containing generic RNA binding motifs is not unexpected and probably results from enhanced binding and concomitant enrichment of these peptides during the panning process.
Thus, our modified MBD-cap protocol allows for low background binding and specific enrichment of methylated fragments from low DNA inputs.
Flow cytometry was used in all the binding assays to monitor the process and enrichment of the selection pools.
In the postprocessing phase, ENIGMA determines relevant condition sets for each module, visualizes their substructure and overlap with other modules, screens the modules for enriched GO categories, suggests potential regulators for the modules based on regulator-module coexpression links and enrichment of TF binding sites, and overlays protein and genetic interaction data.
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