Journal: Cell reports

Article Title: Dissecting gene activation and chromatin remodeling dynamics in single human cells undergoing reprogramming.

doi: 10.1016/j.celrep.2024.114170

Figure Lengend Snippet: Figure 3. Global chromatin de-compaction during heterokaryon reprogramming (A) Representative Voronoi density rendering visual- izations of H2B STORM images of the somatic nu- cleus of control and heterokaryons at different time points after fusion. (B) Quantification of chromatin compaction changes during early heterokaryon reprogramming. Voronoi density values at the 95th percentile corresponding to H2B localizations from somatic nuclei of controls and heterokaryons at different time points after fusion. n = two–four biological replicates. Smaller dots represent individual values, and colored dots are the mean of biological replicates. Two-tailed t test was used to calculate p values and statistical signif- icance using the mean values of biological replicates. (C) Fold change Voronoi density relative to control. The percentage of decrease compared with control is shown for 48 h. Data correspond to the mean and SEM of two–four biological replicates. (D) Homokaryon generation strategy. hFBs were stained against CD90 using antibodies labeled with different fluorophores and fused with PEG. Fused cells containing both fluorescent markers were sor- ted as homokaryons. (E) Representative Voronoi density rendering visual- izations of H2B STORM images of the somatic nu- cleus of unfused fibroblast control and fibroblast homokaryon 48 h after fusion. (F) Voronoi density values at the 95th percentile cor- responding to H2B localizations of fibroblast nuclei at control and homokaryons at 48 h after fusion. n = one biological replicate. Smaller dots are individual values; black dots are the mean values of biological replicates. Error bars are the standard deviations. Two-tailed t test was used to calculate p values and statistical significance. Images in (A) and (E) are color-coded based on Vor- onoi density values from low (blue) to high (red).

Article Snippet: Primary antibodies were diluted in blocking buffer and used as follows: H2B (Proteintech) 1:25; H3K9me3 (Thermo Fisher Scientific) 1:50; H3K27me3 (Thermo Fisher Scientific) 1:100; H3K4me3 (Thermo Fisher Scientific) 1:100; and H3K9ac (Thermo Fisher Scientific) 1:50; and incubated 12h–15 h at 4 C in a humidified chamber.

Techniques: Control, Two Tailed Test, Staining, Labeling