title: GSM7426496: KHOS, EV, HA; Homo sapiens; OTHER
library_construction_protocol: Chromatin profiles of endogenous SS18-SSX1/2, H2AK119ub1 in human synovial sarcoma cells and HA occupancy in osteosarcoma or synovial sarcoma cells expressing MSCV-HA-eGFP-SS18-PGK-Puro, MSCV-HA-eGFP-SS18-SSX1-PGK-Puro and MSCV-HA-eGFP- SSX-C-PGK-Puro was assayed using CUTANA ChIC/CUT&RUN Kit (EpiCypher, 14-1048)following manufacturer's protocol. Briefly, 1 million cells (HS-SY-II, SYO-I or KHOS-240S)were harvested per sample and bound to activated Concanavalin A magnetic beads. Beads werethen incubated at 4 ̊C overnight with 1:50 dilution of antibodies per sample. Chromatin digestion was performed for 2 hours at 4 ̊C. Digestion is then stopped by chelating Ca++ ionsin a buffer containing E.coli DNA for Spike-in. DNA Fragments are then released in solution after a 10 min incubation at 37 ̊C on a ThermoMixer at 500 rpm. DNA Fragments were then purified using CUTANA DNA Purification Kit (EpiCypher). DNA fragments obtained after CUT&RUN were quantified using Qubit dsDNA HS Assay Kit (Invitrogen). 5ng of DNA was used for libraries preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S), SPRIselect beads (Beckman Coulter, #B23317) and NEBNext Multiplex Oligos for Illumina (NEB, Set 1 #E7335S, Set 2 #E7500S). ChIP libraries were done following NEB's guidelines (NEB, E7645S), CUT&RUN libraries were done following CUTANA ChIC/CUT&RUN Kit (EpiCypher, 14-1048) adapted protocol CUT&RUN libraries were sequenced as 75 bp Paired-End reads on Illumina NextSeq 550 platform Mid-Output.