Haynes Lab:Notebook/Synthetic Biology and Bioinformatics for Predictable Control of Therapeutic Genes/2012/01/18

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Preliminary UCSC Genome Browser at ENCODE Run Through

  • After taking some preliminary screen shots of genes within the HepG2 and BJ cell line that showed H3K27me3 methylation signal around the promoter I discovered that it would take entirely too long to scroll through the cell lines in order to find 1000s of genes with this mark on the promoter. I need to email the UCSC Genome Browser at ENCODE in order to find out how I will create a filter in the database that will provide a list of genes where the promoter site shows a high level of the H3K27me3 histone methylation. I will need it to be able to find the beginning of the gene's promoter on the UCSC Genome Browser and then show about 500bps to the left and 500bps to the right of the promoter . Ultimately, I want to be able to navigate through the genes in this cell line that show a significant enough H3K27me3 signal at the promoter (everything else with a low H3K27me3 signal I do not care about).
  • As of now, this is the protocol that needs to be followed
  1. In the Genome Browser set everything in the drop-down controls to hide with the following exceptions: Base Position (dense), UCSC Genes (pack), ENCODE Regulation (show), ENC Histone (show), Conservation (full).
  2. Click on ENCODE Regulation. On the drop down menus select full for Layered H3K27Ac and dense for Txn Factor ChIP. Hide everything else.
  3. Click on ENC Histone. On the drop down menu for UW Histone select full. Hide everything else.
  4. Go to track search and under Cell, tissue or DNA sample enter the cell lines BJ and HepG2. Under Antibody or target protein enter in H3K27me3 (07-449)
  5. Select 3x on the zoom out