title: GSM5511091: SKMEL-1176_HOXA13_rep2; Homo sapiens; OTHER
library_construction_protocol: We performed Cut&Run for the melanoma cell lines SKME-1088, SKMEL-1766, and SKME-1206. For Cut&Run we used 100'000 cells per condition and it was performed as described in Skene et al., Nat Protocol, 2018. We used antibodies against HOXA13 (Invitrogen, #PA5-76440, 1:100), H3K27ac (Active Motiv, #39034, 1:100), IgG (abcam, #ab6709, 1:100) and we added a “no antibody” condition as additional negative control. In brief, 100'000 melanoma cells were collected per condition. Cells were harvested and bound to concanavalin A-coated magnetic beads after 8min incubation at RT on a rotator. Cell membranes were permeabilized with digitonin and the different antibodies were incubated overnight at 4°C on a rotator. Beads were washed and incubated with pA-MN. Ca2+-induced digestion occurred on ice for 30min and stopped by chelation. DNA was isolated using an extraction method with phenol and chloroform as described in Skene et al., Nat Protoc, 2018. KAPA HTP using manufacturers recommendations