title: GSM8439117: MCF7, sciATAC-seq of untreated cycling cells; Homo sapiens; ATAC-seq
library_construction_protocol: Nuclei were extracted and single-cell indexing was performed following the EasySci-ATAC protocol, as described in Supplemental protocol 2 of Sziraki, et al., 2023: https://doi.org/10.1038/s41588-023-01572-y. Briefly, cells were resuspended in 1 mL Nuclei Isolation Buffer (NIB) + 0.1% IGEPAL CA-630 and filtered through a 40 µm filter. Nuclei were stained with Trypan Blue and counted with the EVE Automated Cell Counter; the final concentration was adjusted to 1,000 nuclei/µL using NIB. For each barcode combination, 5,000 nuclei were mixed with 4 µL of barcoded Tn5 and tagmentation was carried out in a thermomixer at 55C for 10 minutes with gentle shaking at 350 RPM.  Following tagmentation, nuclei were put directly on ice to prevent over tagmentation, followed by addition of a stop buffer consisting of spermidine-EDTA. Nuclei were then pooled and redistributed to 96-wells to allow multiplexing via barcoded ligation, followed by a third round of pooling and redistribution to a final barcoding reaction via eight separately barcoded PCR amplifications for library preparation and sequencing on an Illumina NextSeq.