Continuing with the previously loaded GM12878 map, let’s load another Hi-C map and see if we can discover differences between cell lines!
Go to chromosome 21
Click twice to zoom in
Draw a box while holding down the
Alt key so that you’re looking at 28,000 KB to 30,000 KB. Make sure the resolution is 5KB.
File → Open Control
ENCODE IMR90 MboI MAPQ 30 map
Show on the toolbar and select
Normalization on the right to be
As you can see, the regions look quite different!
Another way to examine the data is the VS mode view.
Show on the toolbar
Observed vs Control
Observed (first loaded map - GM12878) is below the diagonal; control (second loaded map - IMR90) is above the diagonal.
Let's explore these differences by bringing in additional ENCODE data.
Show Annotation Panel in the lower right corner
1D Annotations tab
Load Basic Annotations...
Back in the 1D Annotations tab, click
CTCF tracks for both
You’ll notice that there is a peak in the RNA-seq track for IMR-90 on the gene ADAMTS1, and that there’s a peak in the IMR-90 H3K4me3 track; neither of these are present on the respective GM12878 tracks. H3K4me3 is an activation mark. ADAMTS1 encodes a protein involved in fibroblast migration and is inactive in GM12878 but active in IMR90.