Extended Data Fig. 7: Runx1 suppresses EGFR-induced genes in TECs.
From: Thymic alveolar type 2 epithelial mimetic cells revealed by RUNX1 deficiency
a, Location of Runx1 binding sites relative to the transcriptional start site (TSS) from GREAT (Genomic Regions Enrichment of Annotations Tool). b, Motif analysis of Runx1 binding sites from CUT&RUN using MEME-ChIP (Motif Analysis of Large Nucleotide Datasets). The top 5 motifs identified in CUT&RUN were Runx motifs. c, Metascape analysis of genes increased in Runx1-deficient mTECs from scRNA-seq DGE expression comparing total mTECs (all mTEC clusters combined) from Foxn1-Cre(+)/Runx1+/+ (WT) mice versus Foxn1-Cre(+)/Runx1fl/fl (KO) mice. d, Overlay of EGFR-induced genes on scRNA-seq DGE expression comparing total mTECs (all mTEC clusters combined) in WT mice versus KO mice. Blue numbers represent the number of EGFR induced genes in WT mTECs and red numbers represent the number of EGFR induced genes in KO mTECs. e, Overlay of EGFR-induced genes from specific timepoints on scRNA-seq DGE expression comparing total mTECs from WT mice versus KO mice. Blue numbers represent the number of EGFR induced genes in WT mTECs and red numbers represent the number of EGFR induced genes in KO mTECs at each of the indicated timepoints. f-h, Merged genome browser tracks for duplicate CUT&RUN data for IgG, Runx1, and H3K27ac at growth factor receptor gene loci. (d-e) Differentially expressed genes in volcano plots were determined using a two-sided Wilcoxon rank-sum test.
