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Here,  we used genome-scale DNA and RNA imaging to investigate 3D-genome organization in  transcriptionally distinct cell types in the mouse cerebral cortex. We uncovered  a wide spectrum of differences in the nuclear architecture and 3D-genome  organization among different cell types, ranging from the size of the cell  nucleus to higher-order chromosome structures and radial positioning of chromatin  loci within the nucleus. These cell type-dependent variations in nuclear  architecture and chromatin organization exhibit strong correlations with both the  total transcriptional activity of the cell and transcriptional regulation of cell  type-specific marker genes. 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