GSM4728439: DFMC_11112-R1_2F0; Homo sapiens; ATAC-seq
Fragment of frozen tissues (PDX models) or 50 um sections (liver metastases) were cut and resuspended in 300 ul of cold 3-detergent-ATAC-Resuspension Buffer (RSB) containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin. Tissues were dounced 10 times with a loose and a tight pestle each until complete homogenization. The homogenate was then transferred to a 1.5 ml pre-chilled microfuge tube and incubated on ice for 10 minutes to lyse. After lysis, 300 ul of ATAC-RSB containing 0.1% Tween-20 was added and the tubes were inverted to mix. Lysates were filtered through a 40 um cell strainer and nuclei were centrifuged for 10 minutes at 1500 RCF in a pre-chilled (4 ºC) fixed-angle centrifuge. Nuclei were resuspended with 300 ul of ATAC-RSB containing 0.1% Tween-20 and counted with a hemocytometer using Trypan blue stain. ATAC-seq libraries were amplified as described previously (Buenrostro et al.).