Extended Data Fig. 8: TCF-1 ChIP-seq comparison in DPs and DN3s.
From: TCF-1 promotes chromatin interactions across topologically associating domains in T cell progenitors
a. Venn diagram of overlapping and unique bound regions by TCF-1 ChIP-seq thymocytes, DN3s and 3T3TCF-1. b. Local pileup plot of long-range interactions using ultra-deep Hi-C in wildtype and two Tcf7−/− DN3 clones at a subset of CTCF+TCF-1 co-bound, as well as TCF-1-only peaks that gain insulation in Tcf7−/− DN3s. The two classes of peaks were defined using TCF-1 and CTCF ChIP-seq in thymocytes and DPs, respectively as in Fig. 1. These peaks were further selected based on the decrease of average interactions between the upstream and downstream of the peaks by at least 0.05 after TCF-1 deletion. The numbers are the average observed/expected interactions in the upper right square, which is the interactions between the upstream and downstream of the peaks. c. Local pileup interactions in wildtype and Bcl11b deficient naïve CD4 T+ cells at the CTCF and TCF-1 co-bound, as well as TCF-1 only peaks.
