Haynes Lab:Notebook/Synthetic Biology and Bioinformatics for Predictable Control of Therapeutic Genes/2012/02/29

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Closing in on finalizing ENCODE filter

  • Have come to the decision that HepG2 is probably not a good consistent cell line as it is showing random high signals on the genes. BJ is much more consistent so we will focus on that for now and perhaps pick up another cell line along the way (HeLa by any chance?)
  • Discovered that a score of 100 is the lowest possible quality score that can be set, so the score needs to be raised (maybe to 120?)
  • Decided that it is better to get genes that are for sure silenced, so raise the signal value cutoff to 5
  • Need to make a histogram comparing scores in increments of 10 from 100 to 180 to number of hits at signal values 4-7
  • After this is all completed I will run this through GALAXY to hopefully get about 1000 target sites
  • Need to find a gene track to cross my H3K27me3 track with that will provide me with gene names (ReFSeq does not work)
  • GO Terms will follow after



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