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The heat treatment seems to be a positive promoter of surface diffusion (and nanocluster growth), mostly in the early stages of gold layer growth.
Approximately 2 kb of genomic regions both 5' and 3' of the CpG islands clones (or of the transcription start sites for the positive promoter clones) were considered and one or more gene ID were assigned to each clone, if they laid in these regions.
The same regions that showed positive promoter activity in the single time-point studies, −205 to −78 bp and −351 to −78 bp for NXNL1 and Nxnl1, respectively, were found to be important for the observed temporal increase in promoter activity.
The genomic coordinates of the positive CpG islands clones (based on the sequence information retrieved from http://data.microarrays.ca/cpg/) and the −800/+200 regions of the positive promoter clones are supplied in Table S1 GO enrichment analysis was performed at http://bioinfo.vanderbilt.edu/webgestalt with all the 1259 gene id retrieved, but only 1159 were recognized as such.
A methylation ratio > 0.2 was considered as positive promoter methylation.
This large difference in H3K9me3 positive promoter counts among these cells points toward a significantly altered H3K9me3 system for some types of BTSCs as compared to fNSCs.
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There were more H3K4me3 positive promoters than H3K27me3 positive promoters, as opposed to the total peak analysis.
For H3K9me3, there were large differences in number of sites and number of positive promoters across cell types, with the B12 line and fNSCs having many more positive promoters than B25 cells (>2× difference).
Conversely, if there are fewer shared positive promoters, then the core set will be a small fraction of the universe set, because most positive promoters will not be present in all four cell types.
First, there was a substantial core set of positive promoters for each epigenetic mark (H3K4me3: 6742; H3K27me3 1650; H3198meC: 3198; meC: 5360).
Second, a more minor observation concerns the relative number of H3K4me3 and H3K27me3 peaks vs positive promoters.
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