Practice: Interactive Figure

We’re going to recreate a figure! It will be an interactive figure, enabling you to easily verify the findings. You can see an example of an interactive figure here: https://www.cell.com/cell/9802-figure-2

Rao et al., Cell 2017 looked at what happens to genome architecture when you remove cohesin and then introduce it again.

1. Click Load Map → Juicebox Archive

2. Type Rao and select the map Combined Treated (6hr)

3. Double click chromosome 8

4. Zoom in to between 133,800 KB and 134,600 KB. Zoom in as you would in Juicebox Desktop (drawing boxes, double clicking, manually setting resolution) – with the additional capability of pinch zoom on a mobile device.

5. Set the Normalization to Balanced

6. Set the color scale value to 50

Let's now load additional maps

1. Load a map next to this one by clicking the + button. A new window appears to the right.

2. Click Load Map → Select Map File

3. Type Rao and select Combined Treated (6hr) Withdraw (20min)

4. Set Normalization to Balanced

5. Set the color scale value to 15

You know which map window you’re operating on because there’s a dark line around it.

Repeat these steps again, selecting in order: Combined Treated (6hr) Withdraw (40min), Combined Treated (6hr) Withdraw (60min), Combined Treated (6hr) Withdraw (3hr), and Combined Untreated.

The following maps will load below if there’s no room next to the previous map. The final map is deeply sequenced like the first and should have a color scale value of 50. The other maps should have a color scale value of 15.

As you can see, withdrawing the auxin treatment allows loops to form again, as they exist in untreated form! You can play around with color scale and location to verify this wasn’t cherry picked.

Click Load Tracks at the top to load ENCODE tracks alongside these maps. You can also click the icon at the top left to add 2D Annotations to the map. Explore the icons to see what other capabilities exist in Juicebox on the Web!