Nuclei were isolated from snap frozen forebrain tissues or GM12878 cells. Permeabilized nuclei were distributed to 96 wells and tagmentation was carried out to introduce a first barcode combination. After pooling, 25 nuclei were sorted into 384 or 96 wells and a second barcode wqas introduced by PCR. Permeabilized nuclei were distributed to 96 wells and tagmentation was carried out to introduce a first barcode combination (p7 and p5 barcodes). After pooling, 25 nuclei were sorted into 384 or 96 wells and a second barcode (i7 and i5 barcodes) was introduced by PCR. In general, libraries were sequenced on a HiSeq2500 with following read lengths: 50 + 43 + 37 + 50 (Read1 + Index1 + Index2 + Read2). The human mouse mixtures was sequenced on a Miseq with this read lengths: 44 + 43 + 37 + 44 (Read1 + Index1 + Index2 + Read2). The first 8 bp of Index1 correspond to the p7 barcode and the last 8 bp to the i7 barcode. The first 8 bp of Index2 correspond to the i5 barcode and the last 8 bp to the p5 barcode. PLease note that the barcode information was integrated into the read name. combinatorial ATAC-seq