Extended Data Fig. 3: ImmunoGAM contact matrices from replicate mice.
From: Cell-type specialization is encoded by specific chromatin topologies
a, GAM contact matrices centered on the Pcdh gene cluster for mESC, CA1 PGN replicate 2, and VTA DN replicate 2 (Chr18: 36,000,000-39,000,000; 50-kb resolution). ChIP-seq peaks for CTCF15 are shown below the mES cell matrix, showing extensive binding at the Pcdh locus. Dashed lines illustrate differences in contacts between Pcdh-α, -β and -γ genes for different cell types. Scale bars are adjusted to a range between the 0 value and the 99th percentile of NPMI values for each cell type. b, Example matrices for replicate 2 of CA1 PGN and VTA DN, for Chr17: 0-60,000,000 at 50-kb resolution. Dashed lines illustrate vomeronasal (Vmn) and olfactory (Olfr) receptor gene clusters within B compartments, separated by ~35 Mb, are observed in brain cells but not in mES cells. Compartments A/B were classified using normalized PCA eigenvectors2.
