Fig. 1: Mapping nucleome architectures in single cells of mammalian tissue.

a Schematic illustration of the biological features measured by Multiplexed Imaging of Nucleome Architectures (MINA). We imaged cell boundaries, nuclei, nucleoli, 137 different RNA species, 50 TADs in chromosome 19 (Chr19), and 19 consecutive 5-kb loci upstream of gene Scd2 in E14.5 mouse fetal liver tissue sections. b A simplified scheme of the chromatin tracing approach. All genomic regions were first labeled with primary probes (Hyb0), and then sequentially visualized with dye-labeled secondary probes (Hyb1, 2, 3…). c, d (Left panels) Individual and sum images of targeted TADs (c) or loci (d). Images are max projections along the z direction of the 3D image stacks. (Right panels) 3D positions of targeted regions plotted as pseudo-colored spheres connected with a smooth curve. e Raw (left panel) and processed (right panel) images of cell nuclei (blue) and nucleoli (yellow). f A simplified scheme of the RNA profiling approach. Primary probes were first hybridized to the RNA molecules, which encoded each RNA species with a unique 16-bit barcode. Then the barcode was decoded by sequentially visualizing the bits. g (i–iii) Images of RNA molecules in three rounds of secondary hybridization. Images are from a single z position in the 3D image stacks. (iv) All identified RNA molecules in a field of view pseudo-colored based on their gene identities. The yellow boxed region is the same region shown in i–iii. h Raw (top left) and processed (bottom right) images of cell boundaries. i Mean spatial distance matrix of the 50 TADs, with each element showing the mean spatial distance between a pair of TADs. j Inverse Hi–C contact frequency versus mean spatial distance for each pair of TADs. Each dot represents a pair of TADs. k Total RNA copy numbers from imaging versus FPKM values from bulk RNA sequencing for each probed RNA species. Data from 137 RNA species were used to generate (k). Results in Fig. 1 are representative of four biological replicates. Source data are provided as a Source data file.