Here we present a comprehensive map of the accessible chromatin landscape of the 
mouse hippocampus at single-cell resolution. Substantial advances of this work 
include the optimization of a single-cell combinatorial indexing assay for 
transposase accessible chromatin (sci-ATAC-seq); a software suite, scitools, for 
the rapid processing and visualization of single-cell combinatorial indexing 
data sets; and a valuable resource of hippocampal regulatory networks at 
single-cell resolution. We used sci-ATAC-seq to produce 2346 high-quality 
single-cell chromatin accessibility maps with a mean unique read count per cell 
of 29,201 from both fresh and frozen hippocampi, observing little difference in 
accessibility patterns between the preparations. By using this data set, we 
identified eight distinct major clusters of cells representing both neuronal and 
nonneuronal cell types and characterized the driving regulatory factors and 
differentially accessible loci that define each cluster. Within pyramidal 
neurons, we identified four major clusters, including CA1 and CA3 neurons, and 
three additional subclusters. We then applied a recently described 
coaccessibility framework, Cicero, which identified 146,818 links between 
promoters and putative distal regulatory DNA. Identified coaccessibility 
networks showed cell-type specificity, shedding light on key dynamic loci that 
reconfigure to specify hippocampal cell lineages. Lastly, we performed an 
additional sci-ATAC-seq preparation from cultured hippocampal neurons (899 
high-quality cells, 43,532 mean unique reads) that revealed substantial 
alterations in their epigenetic landscape compared with nuclei from hippocampal 
tissue. This data set and accompanying analysis tools provide a new resource 
that can guide subsequent studies of the hippocampus.