Hello Guys, Recently I got my H3K4me1 NGS data. Unfortunately seems like the ChiP-experiment didn't work out (as peaks are super-low and similar to the Input 😭).
I'm currently trying to understand how to, eventually, overpass the H3K4me1 as my H3K27Ac sequencing are very good in both CTR and Treated. I'm working in Mouse, in a pretty specific cellular population (similar but not definable as "Fibroblast") and all I have is H3K27Ac and Nuclear accessibility (NA-seq) DATA.
I was desperately trying to get some "Enhancers annotation" but it seem to be cell specific (to a certain degree). This is the site, if you are interested: http://www.enhanceratlas.org/index.php
Given that my cell is pretty "Niche" I was starting to think to simply integrating Differentially H3K27Ac Peaks covered with Na site 🤔.
Do you think is a viable strategy? Reading this article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4517609/ I realized that Nuclear accessibility and H3K4me1 are both markers of eventually primed Enhancers. H3K27Ac is what should be essential to my goal, isn't it?
Thanks in advance