Fig. 1. Deregulated thymic development in Satb1 cKO mice.
a Fold-enrichment distribution of peaks from all available blood ChIP-seq datasets based on ChIP-Atlas42 at WT H3K27ac loop anchors over random permutation and the corresponding p values. Peaks from SATB1 ChIP-seq datasets (highlighted in red) were enriched at the anchors of regulatory chromatin loops. b Methylene blue stained thymus sections from WT and Satb1 cKO mice displaying a disrupted thymic environment in the Satb1 cKO mouse (C: cortex, M: medulla, CM: corticomedullary region; scale bar 50 µm). The experiment was repeated 4 times in total with similar results. c Transmission electron microscopy thymic cryosections (representative of 4 biological replicates) indicating thymocytes with disrupted intercellular contacts in the Satb1 cKO cells. Cell borders are indicated by yellow dashed lines and green and magenta arrows show examples of intact and disrupted intercellular contacts, respectively. Figures d, g, h, i: Flow cytometry analysis to characterize cell populations in the thymus, spleen, lymph node and pancreas of WT and Satb1 cKO animals, respectively. Gating for CD4/CD8, CD62L/CD44 and Annexin V/PI experiments were G1, G2 and G3, respectively (Supplementary Fig. 3b). Images are representative of the analyzed group and percentages represent the mean. All experiments are summarized in Supplementary Fig. 3c. e Number of thymocytes in WT and Satb1 cKO mice. The horizontal lines inside violins represent the 25th, 50th and 75th percentiles. The red circle represents the mean ± s.d. P values by two-sided Wilcoxon rank sum test. f Neonatal thymi from WT and Satb1 cKO mice were cultivated for 30 hours. An image was taken every hour to monitor the rate of T cell exit from the thymus. The final result represents an average from two animals for each genotype. The error bars represent the standard error of the mean. j Differences in the cytokine milieu in the blood serum of n = 5 WT and n = 11 Satb1 cKO (SKO) animals measured with bead-based immunoassay. Note the elevated IL17 response and increased inflammatory cytokines. The red circle represents the mean ± s.d. P values by two-sided Wilcoxon rank sum test. All data analyzed can be found in the source data file. k Overlap enrichment of T cell subset signature genes and differentially expressed genes in Satb1 cKO. Overlapping genes are depicted in the source data file. l Expression changes of DN, DP and SP T cell subset signature genes. DP signature genes displayed the lowest RNA levels in Satb1 cKO, indicating the specificity of the SATB1 regulatory function at the DP stage. P values by two-sided Wilcoxon rank sum test, non-adjusted for multiple comparisons. The boxplots show median with the top and bottom edges of the box representing the 75th and 25th percentiles, respectively. The whiskers represent the most extreme values that are within 1.5 times the interquartile range of the 25th and 75th percentiles. Outliers outside the whiskers are shown as dots. The exact number of features analyzed can be found in the source data file.