Welcome to Hi-C project at Ren Lab!
Hello! Welcome to the Ren Lab mouse ENCODE website. We have ChIP-Seq and RNA-Seq in 19 mouse tissues in UCSC Genome Browser and Hi-C data from mouse cortex that you can access via this website. This tutorial will help guide you through using the browser to view particular regions of interest in the data. Let's get started!
First, open a new window with the URL: http://chromosome.sdsc.edu/mouse/. This page is the home page for the mouse ENCODE data where you can view the abstract of our paper, as well as links to the data, publication information, and contact information in case you have any questions or suggestions. To view the data, click on the data tab:
You should now be at the following page, which we call the data access page:
From here you can access the data. We have two choises to choose from in the drop down menu, raw Hi-C signals from mouse cortex and normalized Hi-C signals. You can also choose a chromosome of interest from the neighboring drop down box.
To view a particular region, you will need to know the genomic coordinates of the region you are interested in (we don't have the capabilities yet of allowing you to search for a gene of interest and then display just that gene). So, this means you need to have a genomic region of interest to search for. If you don't know the coordinates off the top of your head, look up your favorite region in the UCSC Genome Browser (http://genome.ucsc.edu/) and paste the coordinates into this page (note: we use the mm9 assembly for mouse and hg18 assembly for humans). Also, the way we make the heatmaps is by binning the data into 20kb bins, so your coordinates should be a multiple of 20,000. To start, lets look at a region surrounding the Sox2 gene in mouse ES cells. Enter in the following coordinates using mouse ES cell and chr3 from the drop down menus: start position = 33000000 end position=37000000 (no commas please). Your page should look like this:
Don't worry about the "intensity cutoff" boxes for now, we will get to those later. If everything looks right, click the "check button" and your region should load! You should now be looking at a new page:
This is the heat map surrounding the Sox2 region. The heat map is viewed in a manner similar to a linkage disequilibrium plot, where the interaction between two loci is viewed as the point where the diagonals originating from each locus intersect on the heat map. Below the heat map is data from the UCSC genome browser containing information on domain, the directionality index, and ChIP-Seq data. Note: the UCSC genome browser session may not be lined up perfectly with the heat map unless you make it so. In order to do so, you need to scroll sideways until the edges of the UCSC data line up with the edges of the heat map, as shown below:
Hopefully, you can see something here or at your favorite region of the genome that will greatly aid your research. If not, we at least hope that you agree that Hi-C data is pretty cool! Now let's try some more advanced options. Go back to the previous page in your browser (the data access page). See the boxes at the bottom that say "min intensity cutoff (Optional)" and "max intensity cutoff (Optional)"? We are going to play around with those to change how we view that data.
But first, an explanation is in order. The two values ("min and max") are important for the color intensity of the heat map that is generated. If you don't enter anything here, there are default values that we think work reasonably well for viewing the data, but there may be additional features that are better seen with different color schemes. In brief, the numbers you enter here change the intensity and contrast of the heat map. Literally speaking, the number correspond to the number of reads that map between any two bins. If the number of reads is below the minimum cutoff, the heat map will be white for that interaction. If the number is equal to or greater than the maximum value, the color will be red. Anything in between will be some shade of red/pink. Let try an example. The previous heat map you generated at the Sox2 locus used the default cut off values of 5 (min) and 50 (max). The heat map looked like this:
Try entering new color values of 15 (min) and 50 (max), the data entry should look like this:
Click the "check button" and you should see a new heat map, that looks like this:
We hope you can see some of the subtle changes that have taken place in viewing the data with a higher minimum cut off. The interactions that stand out in this heat map may be considered to be the relatively "strong" interactions. We hope that this has given you a reasonable understanding of how to use our Hi-C data viewer. If you have any questions, comments, or suggestions, please don't hesitate to email us. Enjoy!