Supplementary Figure 2: Foxp3 binds similar loci in resting Treg cells and activated Treg cells. | Nature Immunology

Supplementary Figure 2: Foxp3 binds similar loci in resting Treg cells and activated Treg cells.

From: Inflammation-induced repression of chromatin bound by the transcription factor Foxp3 in regulatory T cells

Supplementary Figure 2

(a) Quantitative assessment of Foxp3 ChIP in resting and activated Treg cells. Peaks were called in both resting and activated cells and RPM was computed in each condition on the union of peaks. Data was quantile normalized prior to averaging across n=4 aTreg and n=2 rTreg replicates. Raw data were also analyzed by negative binomial modeling as described in main text and methods. (b) Same as A, except x- and y-axes show replicate-to-replicate variation for aTreg (left) and rTreg (right) Foxp3 ChIP-seq RPM data. This analysis demonstrates that the variation observed in A does not surpass reproducibility variation. (c) Analysis of the distribution of RPM-fold changes shows that the rTreg-vs-aTreg comparison does not surpass that observed in reproducing the data in either condition.

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