BUCK LAB

Igor Pro Chromosome-View Files

Click below to download any of the chromosome-specific files

Chromosome 1 (451 Mb)
Chromosome 2 (357 Mb)
Chromosome 3 (198 Mb)

How to view these files

These three files were created in Igor Pro Version 6, which is commercial software. Fortunately, WaveMetrics, Inc. (creators of Igor Pro software) provides a free viewer for Igor Pro files. That free viewer is simply the free demonstration version of Igor Pro, which can be downloaded from http://www.wavemetrics.com/support/demos.htm. There are no forms required to download the demo; downloading is anonymous. The demo runs on Windows XP, Vista and 7, and it also runs on Macintosh OS X 10.4 and later. The demo is fully functional for 30 days after installation. Beyond that time (in the absence of a purchased license), it becomes impossible to save files or to copy to other programs.However, the viewing features remain fully functional.

Extensive online help, including a comprehensive manual and a tutorial in PDF format, accompany the Igor Pro demo download. Please read that information if you have detailed questions about the workings and capabilities of Igor Pro software. Here we provide some simple instructions for scanning along a chromosome at any desired resolution.

When you open any of the three chromosome files, you will see a graph that looks something like this:

image4

The features of this graph are identical to those of Supplementary Figures S5 and identical to those of Additional Figure 1.

The default graphs, with which the chromosome files open, show a stretch of 4 kbp on the indicated chromosome. This resolution is optimal for seeing the locations of individual nucleosomes and other MNase-protected structures near TSSs, TTSs or replication origins, but this resolution does not allow one to see a "bigger picture". To change the resolution and/or to navigate to a different position on the chromosome, select "Set Axis Range..." under the Graph menu. This will bring up a dialog box like the one shown here:

image5

In the "Axis" pop-up menu (upper left corner), select "bottom" (in order to make adjustments to the horizontal [bottom] axis of the graph). Then, under "Manual Range Settings" (center of the dialog box), enter the chromosomal coordinate that you would like to see at the left edge of the graph under "Manual Min", and enter the coordinate that you would like to see at the right edge of the graph under "Manual Max". Ignore everything else. It may be useful to know that the length of chromosome 1 is 5,579,133 bp; the length of chromosome 2 is 4,539,804 bp; and the length of chromosome 3 is 2,452,883 bp.

It is also possible to pan along the chromosome. You may find panning easier if the resolution is set so that the horizontal span of the graph includes a larger distance, say 50 kbp. Here is how the graph appears when, according to the instructions in the preceding paragraph, the value of "Manual Min" is set to 2350000, and the value of "Manual Max" is set to 2400000:

image2

At this lower resolution, one cannot detect individual nucleosomes in panels (i) or (ii). However, one can better see patterns in the data obtained by microarray (panels (iii) and (iv)).

To pan horizontally, one needs to hold down the Shift and Option keys (Macintosh) or the Shift and Alt keys (Windows), then move the cursor over the center of the graph until it changes to a hand (the graph window must be the active window), then drag to the left or right. The following picture shows the results of dragging to the left far enough to reveal another putative replication origin (AT3066, accompanied by a peak of pre-RC proteins).

image1

After locating a feature of interest, one can then change the scale to see that feature at higher resolution. Here is the result of setting "Manual Min" to 2307000 and "Manual Max" to 2311000 (a span of 4 kbp):

image3

Additional, more sophisticated methods for panning, zooming, etc., are described in the Igor Pro instruction manual and help files. If you have questions, you can also send an e-mail inquiry to one of the corresponding authors (JAH or MJB).