Figure 4
Thawed Treg cells demonstrate comparable TF activity to fresh cells. ATAC-seq was performed on sorted resting and stimulated fresh and thawed Treg cells. (a) Correlation of stimulation-responsive chromatin accessibility changes in fresh and thawed Treg cells (expressed as fold changes in reads in peaks between resting and stimulated states). Differentially accessible genomic loci between resting and stimulated states were defined as genes having an FDR of less than 0.05 and log-fold change that is significantly greater (red) or lower (blue) than 1.2 (equivalent to a 2.3-fold difference between conditions). ATAC-seq peaks were annotated to the nearest TSS and common differentially accessible peaks with a log-fold change that is significantly greater/lower than 4 are annotated by gene symbol. Top 20 common differentially accessible Treg signature genes (Ferraro et al. 37) are highlighted in green. (b–d) Histogram comparing fragments from fresh and thawed samples at FOXP3 (b), CTCF, RUNX1, CREB1, GATA3, IRF1 and YY1 binding motifs during resting (c) and stimulated (d) states. TF occupancy signal is computed on the genome-wide ATAC-seq footprints matching the corresponding motifs obtained from JASPAR database. Histograms are generated from Treg chromatin accessibility signals computed from pooled sequencing data representative of three donors.
