Fig. 1

txci-ATAC-seq generates high-quality single-cell ATAC libraries at high throughput. a Schematic of molecular details of txci-ATAC-seq library generation. b Experimental workflow for txci-ATAC-seq barnyard library generation. After 96-plex tagmentation, nuclei are overloaded on a 10X Chromium microfluidics device. Following nucleus encapsulation in the formed droplets, 10% of the GEMs can be used for quality control and the remaining 90% for data analysis. c-e) txci-ATAC-seq QC metrics for human (GM12878) and mouse (CH12) cell lines supplemented with SBS primer during in-droplet PCR. c “Knee” plot showing the unique reads (log₁₀ scale) against the rank of each barcode (log₁₀ scale) ordered from most unique reads (left) to least (right). The dashed line indicates the threshold (1000 reads) used to identify cell barcodes (orange points). d Scatter plots showing the number of unique reads mapped to either the human or mouse genome for both true and pseudo-barnyard experiments. Values were log₁₀-transformed after adding a pseudo-count of 1 to all values. The percentage shown in the true barnyard panel (6.6%) represents the estimated collision rate. e Scatter plots showing the FRiDHS against the estimated complexity for each cell barcode detected as either mouse (blue) or human (red) cell. The estimated complexity is shown on a log₁₀ scale