GSM8112053: KP-N-YN  PRRX1-induced cells-YAP1-R2; Homo sapiens; OTHER
500,000 cells/sample were harvested and bound to concanavalin A–coated magnetic beads. Cells were permeabilized with 5% digitonin. After overnight incubation with echa antibody, beads were washed and incubated with pAG-MNase produced at CNIO (Protein Production Unit). Cells were chilled to 0 °C and digestion was initiated by adding Ca2+. Reactions were stopped by chelation including spike-in DNA and the DNA fragments released by cleavage were extracted from the supernatant. Library preparation and paired end sequencing for KELLY, LAN-1, and SK-N-AS  cells were performed at the CNIO Genomics Unit; experiments with the KP-N-YN inducible cells were performed at the Center for Applied Genomics (CHOP). DNA samples were processed through subsequent enzymatic treatments for end-repair, dA-tailing, and ligation to adapters with "NEBNext Ultra II DNA Library Prep Kit for Illumina" (NEB ref.E7645). Adapter-ligated libraries were completed by a limited-cycle PCR, with 63º T(ann/ext) for 10s, and extracted with a [single] double-sided SPRI size selection. Resulting average fragment size is 325 bp from which 120 bp correspond to adaptor sequences. Libraries were applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument by following manufacturer's recommendations.