Fig. 1: ImmunoGAM captures cell-type-specific chromatin contacts in the mouse brain.
From: Cell-type specialization is encoded by specific chromatin topologies
a, ImmunoGAM was applied to three brain cell types: OLGs, DNs and PGNs (one independent biological replicate for OLGs and two replicates for DNs and PGNs). b, Schematic of the ImmunoGAM workflow. OLGs were selected by immunolabelling with GFP, DNs with tyrosine hydroxylase and PGNs using tissue morphology. Nuclear profiles were laser microdissected, each from a single cell, with three collected together, as described for multiplex-GAM9. c, Example of cell-type-specific contact differences at the Pcdh locus (chromosome 18: 36–39 Mb). GAM matrices represent co-segregation frequencies of 50-kb genomic windows using normalized pointwise mutual information (NPMI). Dashed lines illustrate cell-type differences. NPMI scales range between 0 and 99th percentile per cell type. Contact density heatmaps represent insulation scores using 100–1,000 kb square sizes. RNA-seq and ATAC-seq tracks represent normalized pseudobulk reads from scRNA-seq and scATAC-seq, respectively, except for bulk ATAC-seq from mES cells. d, Strong contacts between Vmn and Olfr receptor gene clusters on chromosome 17 (0–60 Mb) within B compartments (Comp.), separated by ~35 Mb, are observed in brain cells but not in mES cells. Compartments A and B were classified using normalized PCA eigenvectors2.
