Ephrin-B2 Deletion in GABAergic Neurons Induces Cognitive Deficits Associated with Single-Nucleus Transcriptomic Differences in the Prefrontal Cortex
A total of 11,308 single nuclei were sequenced. After quality filtering (Methods, Supplementary Fig. 3A, 4A-4C), 11,090 high-quality nuclei were obtained, including 5,336 cells from EB2-flox mouse and 5,754 from EB2-vGATCre mouse. These nuclei were grouped into 17 cell clusters (Supplementary Fig. 4D-4H), which were further assigned to 9 major cell types based on cell-type-specific markers: excitatory neurons (Slc17a7+), inhibitory neurons (Gad2+), astrocytes (Gja1+), microglia (C1qa+), oligodendrocytes (Aspa+), oligodendrocyte precursors (Pdgfra+), smooth muscle cell (Uaca+), endothelial (Flt1+) and ependymal (Dynlrb2+) cells (Fig. 4A, 4C, supplementary Fig. 3B). Overall design: We dissociated cells from brain slices per brain (+2.1-+1.1 AP to bregma) from the individual mouse.