Locating ChIP-seq peaks from ENCODE

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  1. Go to the UCSC website [1]
  2. Go to the ENCODE option on the left-hand side of the page
  3. Click on the Explore ENCODE data at UCSC picture
  4. Scroll to ChIP-seq and click “view matrix”
  5. Find your protein of interest (it is important to note the cell line used in the experiment and what species this DNA is from)
  6. Click on the appropriate tracks for viewing
  7. Click return to browser
  8. Enter your gene of interest in the search bar and click ‘go’ to determine if there are peaks indicating potential GREs or motifs of interest. If there are you can zoom in/out to find where these peaks are located in respect to your gene of interest. It is a good idea to take a picture of this location for future reference and to take note of the number of the particular peak if there are multiple ones for that gene.
  9. Right click on the peak (these are labeled ‘peak#' on the left hand side and look like a grey bar) and select ‘get DNA for peak#’
  10. Add bp to either side if necessary and click ‘get DNA’
  11. Design primers for genes you believe your protein is bound to RT-PCR primer design for ChIP
      • For example, when looking for glucocorticoid-induced GRE peaks you would choose the glucocorticoid receptor, Nr3c1. I would click on the Dex treated tracks to view. This experiment was performed in A549 human lung cells so if you are performing ChIP in mouse cells you would need to BLAT the peak sequence against mouse to get the correct sequence for designing primers