Fig. 1: sciMAP-ATAC schematic and performance.

a sciMAP-ATAC workflow. Cryosectioning of alternating 20 µm (histological) and 100–300 µm (sciMAP-ATAC) slices are obtained. Thin (20 µm) slices are stained and imaged for use in spatial registration (scale bar, 1 mm) to a reference atlas (Allen Mouse Brain Atlas: http://atlas.brain-map.org/atlas?atlas=1&plate=100960312, ref. ²⁵). Thick (100–300 µm) slices are carried through high-density microbiopsy punching (100–500 µm diameter) in the cryostat chamber. Punches are placed directly into wells of a microwell plate for nuclei isolation, and washed prior to splitting into multiple wells for indexed transposition and the sci-ATAC-seq workflow. b Four punch volumes were assessed for nuclei yield using either a 250 or 500 μm diameter punch on a 200 or 300 μm thick section. Total nuclei isolated for each punch is shown on the left, and normalized for tissue voxel volume on the right, representing the efficiency of extraction from each punch, for punches with dimensions 250 ×200 μm (n = 48), 250 × 300 μm (n = 15), 500 × 200 μm (n = 46), and 500 × 300 μm (n = 7). Center line represents median, lower and upper hinges represent first and third quartiles, and whiskers extend from hinge to ±1.5 × IQR. c Passing reads per cell from sci-ATAC-seq (n = 4102 cells examined from a single mouse brain experiment) and sciMAP-ATAC (n = 15,552 cells examined from two independent mouse brain experiments), which are comparable at the level of depth sequenced. Center line represents median, lower and upper hinges represent first and third quartiles, whiskers extend from hinge to ±1.5 × IQR, individual cells represented as colored dots. d ATAC read signal at transcription start sites (TSSs) and surrounding base pairs (bps) for sci-ATAC-seq and sciMAP-ATAC. Enrichment for sci-ATAC-seq is greater than that of sciMAP-ATAC, likely due to increased processing time of isolated nuclei prior to transposition. e UMAP of sciMAP-ATAC and sci-ATAC-seq libraries from mouse brain group closely together. Asterisk indicates a population of 734 cells, derived from spinal cord, which was not sampled during microbiopsy punching. Source data are provided as a Source data file.