Preliminary Analysis: Using the UCSC Genome Browser and ENCODE Data
- The first part of using bioinformatics in this project will be using the genome browser to visualize chromatin mapping data within the human genome sequence. The following protocol was followed as an example to find the annotated chromatin marks of H3K27me3 in human embryonic stem cells.
- Go to the UCSC Genome Browser at http://genome.ucsc.edu/cgi-bin/hgGateway.
- Enter a gene or region under search term. For instance, try “chr21:34398216-34401503” (these are the coordinates for the RefSeq annotation of the Polycomb-silenced OLIG2 gene). Click “submit.”
- A human genome browser window that shows the selected region should appear. Click the “hide all” button to hide all of the information.
- Under Genes and Gene Prediction Tracks, set RefSeq Genes to “full” and click the “refresh” button. The annotation of genes in the region you selected should appear in the browser window. Repeat this step for other features, if desired.
- To find ChIP-seq data from a publicly shared ChIP-seq experiment, click the “track search” button. You will navigate away from the browser, but your coordinates will remain the same. In the next window, click the Advanced search tab. # For the first and, set the menu to “Antibody or target protein”; for is among, set the menu to the chromatin mark(s) of interest. For instance, try H3K27me3 (07-449).
- For the second and, set the menu to “Cell, tissue, or DNA sample”; for is among, set the menu to the cell type of interest. For instance, try H1-hESC (human embryonic stem cells). For detailed information on cell types, click the “Cell, tissue, or DNA sample” link.
- Click the “search” button. In the list of results select one or more tracks and set each to “full.” Tracks designated as “Peaks” or “Hotspots” will show the mapping data as low-resolution, horizontal bars. Tracks designated as “Signal” will show signal intensities as high-resolution, vertical bars.
- Click the “View in Browser” button.
- If you are viewing Signal tracks where high values are cut-off by a red bar, right-click on the track in the genome browser and select configure. Select “auto-scale to data view” on the drop down list titled “Data view scaling.”
- There were two tracks that resulted from the search for H3K27me3, and the view in the genome browser when the two tracks were viewed in "full" should look something like the following figure.
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Using Public Data to Predict and Control Stem Cell Development
