GSM8447289: Bulk ATAC kidney cortex; Homo sapiens; ATAC-seq
To isolate nuclei, 2g of fresh kidney cortex fragments were homogenized in buffer (250mM sucrose, 10mM Tris pH 7.5, 3mM MgCl2, 0.1% NP40) using a gentleMACS M Tube (Miltenyi Biotec, 130-093-237) and gentleMACS dissociator program E.01. The homogenate was filtered through a 200um filter, 100um filter, and pelleted by centrifugation. The Omni-ATAC protocol was used (Corces et al. Nature Methods 2017), with minor modifications as follows. Nuclei from 2g of tissue were resuspended in 1ml of ATAC-Resuspension Buffer (RSB) containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin and incubated on ice for 3 minutes. 15ml RSB with 0.1% Tween was added to the sample to dilute detergents. Nuclei were passed through a 40μm filter and subsequently counted. 100,000 nuclei were pelleted and resuspended in 95uL of transposition buffer (33uL PBS, 1uL 1% Digitonin, 1uL 10% Tween-20, 10uL Nuclease Free Water, 50uL 2x TD buffer: 20mM Tris pH 7.5, 10mM MgCl2, 20% Dimethyl Formamide) with 10μl of transposase (Illumina, 20034197).