Extended Data Fig. 5: An integrated multimodal census and atlas of cell types in the primary motor cortex of mouse, marmoset and human.

The mouse MOp consensus transcriptomic taxonomy at the top is used to anchor cell type features in all the other modalities. Subclass labels are shown above major branches and cluster labels are shown below each leaf node. Confusion matrices show correspondence between the mouse MOp transcriptomic taxonomy (116 clusters) with those derived from other molecular datasets, including mouse MERFISH (95 clusters), the integrated mouse molecular taxonomies by SingleCellFusion (SCF) (56 neuronal clusters) or LIGER (71 clusters), and the human and marmoset transcriptomic taxonomies (127 and 94 clusters, respectively). Cells within each taxonomy were either mapped to the reference (MERFISH, SCF, LIGER) or shared common cells via integration (Human, Marmoset). Color code corresponds to the fraction of cells in each column mapped to or shared with each reference cluster, and each column summed up to 1. These mapping relationships between the mouse consensus transcriptomic taxonomy and other taxonomies are summarized in an overview panel in Figure 9e. Using Patch-seq and connectivity studies, many transcriptomic neuronal types or subclasses are annotated and correlated with known cortical neuron types traditionally defined by electrophysiological, morphological and connectional properties. Relative proportions of all cell types within the mouse MOp are calculated from either the snRNA-seq 10x v3 B dataset (horizontal bar graph) or the MERFISH dataset (vertical bar graph to the right of the MERFISH matrix). The numbers of cCRE-gene pairs in modules corresponding to neuronal subclasses identified by Cicero from the scRNA-seq and snATAC-seq datasets are shown at the bottom of the SCF matrix.