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Fig. 4 | Genome Biology

Fig. 4

From: A transient ischemic environment induces reversible compaction of chromatin

Fig. 4

Nearest neighbor characterization of OND-induced chromatin compaction. Nearest neighbor analysis was used to describe the extent of chromatin compaction upon deprivation of oxygen and nutrients using three internal regions of interest (ROIs; outlined with dashed boxes), as illustrated for an HL-1 cell subjected to 1 hour of OND (a). Results were generated for each experimental condition using three ROIs per nucleus and three nuclei per determination. b The effect of the number of nearest neighbors evaluated on the distance to the analyzed position is shown as a histogram and as a box plot showing the median and range of distribution of values for untreated cells. c The extent of chromatin compaction as cells transition from normal conditions through OND and in recovery from OND, using the distance to 500 nearest neighbors, with the median and range of distribution shown above each histogram. The proportion of bins with a distance to 100 nearest neighbors ≥ 80 nm is shown as a bar on the right of each panel. d The relationship between the number of nearest neighbors used in the analysis to the median distance to the set of nearest neighbors for each experimental condition

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