Data from: ATRX promotes maintenance of herpes simplex virus heterochromatin during chromatin stress

Cabral JM, Oh HS, Knipe DM

Date Published: November 30, 2018

DOI: https://doi.org/10.5061/dryad.95fs76f

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Title Colocalization Distribution Data Analysis Script
Downloaded 6 times
Description MATLAB script uses nuclear masks and foci center x,y coordinate data from each channel (results from Foci Detection and Colocalization software) to determine distances of nearest neighbor foci in a second channel from foci in the reference channel and generate distance frequency data. The script then generates the same number of random x,y points within the nuclear mask as were detected in the second channel. The distances from the centers of reference channel foci to nearest neighbor random points is then calculated and reported to within a user defined user defined radius of each reference focus. The resulting frequency distributions of reference-to-test channel distances and reference-to-random points are compared by the non-parametric Kolmogorov-Smirnov test. If the test rejects the null hypothesis at 5% significance, the test returns a value of 1, and 0 if the null hypothesis is not rejected. The test also returns an asymptotic p-value and a list of distances in pixel values which can then be plotted and further analyzed using GraphPad Prism (as it was here) or other data analysis packages.
Download ColocCode_V02.zip (3.617 Kb)
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Title Foci Detection and Colocalization 1052 Software.
Downloaded 2 times
Description Foci Detection and Colocalization Software. The Image and Data Analysis Core (IDAC) at Harvard Medical School developed a custom MATLAB based software for nuclear foci and colocalization detection in microscopy images based upon their previously described nuclear foci detection software. In brief, unaltered images are analyzed by the software to detect signal intensity over a set threshold to isolate foci from background. The software then uses DAPI staining to generate a mask that defines nuclear areas in the image. Only foci above the fluorescence threshold and within the nuclear masks are scored. The software determines colocalization based on the distance between the centers of nuclear foci in a reference channel to foci in other channels of the image.
Download ColocMatlabScripts.zip (292.5 Kb)
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When using this data, please cite the original publication:

Cabral JM, Oh HS, Knipe DM (2018) ATRX promotes maintenance of herpes simplex virus heterochromatin during chromatin stress. eLife 7: e40228. https://doi.org/10.7554/elife.40228

Additionally, please cite the Dryad data package:

Cabral JM, Oh HS, Knipe DM (2018) Data from: ATRX promotes maintenance of herpes simplex virus heterochromatin during chromatin stress. Dryad Digital Repository. https://doi.org/10.5061/dryad.95fs76f
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