Extended Data Fig. 6: Distinct spatial organization and chromatin structure per cell type.
From: Visualizing DNA folding and RNA in embryos at single-cell resolution
a, t-SNE 2D projection of the RNA expression data, clustered with DBSCAN (see Methods). Annotations identified by manual inspection are indicated by matching colours and numbers (labelled on the right). This number/colour legend is used for all panels. b, The relative embryonic spatial positions of cells in each group shown for three embryos. c, Distance maps from ORCA for each assigned group. d, Normalized distance maps (observed minus expected distance) for each group. The expected distance accounts for the polymer nature of DNA, whereby sequences closer in linear position along the genome are expected to be closer together in 3D space. The expected distance was calculated by fitting a power law to the distribution of 3D separation distances between barcodes as a function of their linear separation for all data in all cells.
