SRX13126419 GSM5688961_r1 SRP345841 PRJNA780001 SRS11061296 GSM5688961 GSM5688961 OTHER GENOMIC other CUT&RUN was performed as described by Skene et al 2017). 300,000 cells per sample were isolated and anti-V5 antibody (Invitrogen) was used for all samples. pAG-Mnase was added to each sample to a final concentration of 700ng/ml. Chromatin digestion was performed after addition of CaCl2 and DNA digestion was halted Digestion was allowed to proceed on ice for 30 minutes and halted by the addition of 2X Stop Buffer (340mM NaCl, 20mM EDTA, 4mM EGTA, 50 micrograms/ml RNase A, 50 micrograms/ml glycogen). DNA was extracted by the addition of SDS (final concentration 0.1%) and proteinase K (final 10 micrograms/ml) and incubating at 55 degrees for 1 hour. The material was extracted with one equivalent volume of Phenol/Chloroform/Isoamyl Alcohol 25:24:1 (ThermoFisher Scientific), precipitated and washed with 100% ethanol. DNA was resuspended in 150 microliters of water followed by the addition of 75 microliters of AMPure XP beads (Beckmann Agencourt). Beads were mixed and incubated for 5 minutes, added to a magnet for 2 minutes and the supernatant was collected as size selected fragments. The DNA was precipitated by adding 700 microliters of ethanol and 1 ul of 20 mg/ml glycogen and spun at 16000xg for 10 minutes. The pellet was washed with 70% ethanol and resuspended in 20 microliters of 10mM Tris-HCl, 1mM EDTA. Libraries were prepared using the Swift Biosciences Accel-NGS 2S Plus DNA Library kit according to manufacturer's instructions. Libraries were PCR amplified for 12 cycles according to the manufacturer's instructions. NextSeq 500 SRX13126420 GSM5688962_r1 SRP345841 PRJNA780001 SRS11061295 GSM5688962 GSM5688962 OTHER GENOMIC other CUT&RUN was performed as described by Skene et al 2017). 300,000 cells per sample were isolated and anti-V5 antibody (Invitrogen) was used for all samples. pAG-Mnase was added to each sample to a final concentration of 700ng/ml. Chromatin digestion was performed after addition of CaCl2 and DNA digestion was halted Digestion was allowed to proceed on ice for 30 minutes and halted by the addition of 2X Stop Buffer (340mM NaCl, 20mM EDTA, 4mM EGTA, 50 micrograms/ml RNase A, 50 micrograms/ml glycogen). DNA was extracted by the addition of SDS (final concentration 0.1%) and proteinase K (final 10 micrograms/ml) and incubating at 55 degrees for 1 hour. The material was extracted with one equivalent volume of Phenol/Chloroform/Isoamyl Alcohol 25:24:1 (ThermoFisher Scientific), precipitated and washed with 100% ethanol. DNA was resuspended in 150 microliters of water followed by the addition of 75 microliters of AMPure XP beads (Beckmann Agencourt). Beads were mixed and incubated for 5 minutes, added to a magnet for 2 minutes and the supernatant was collected as size selected fragments. The DNA was precipitated by adding 700 microliters of ethanol and 1 ul of 20 mg/ml glycogen and spun at 16000xg for 10 minutes. The pellet was washed with 70% ethanol and resuspended in 20 microliters of 10mM Tris-HCl, 1mM EDTA. Libraries were prepared using the Swift Biosciences Accel-NGS 2S Plus DNA Library kit according to manufacturer's instructions. Libraries were PCR amplified for 12 cycles according to the manufacturer's instructions. NextSeq 500 SRX13126421 GSM5688963_r1 SRP345841 PRJNA780001 SRS11061297 GSM5688963 GSM5688963 OTHER GENOMIC other CUT&RUN was performed as described by Skene et al 2017). 300,000 cells per sample were isolated and anti-V5 antibody (Invitrogen) was used for all samples. pAG-Mnase was added to each sample to a final concentration of 700ng/ml. Chromatin digestion was performed after addition of CaCl2 and DNA digestion was halted Digestion was allowed to proceed on ice for 30 minutes and halted by the addition of 2X Stop Buffer (340mM NaCl, 20mM EDTA, 4mM EGTA, 50 micrograms/ml RNase A, 50 micrograms/ml glycogen). DNA was extracted by the addition of SDS (final concentration 0.1%) and proteinase K (final 10 micrograms/ml) and incubating at 55 degrees for 1 hour. The material was extracted with one equivalent volume of Phenol/Chloroform/Isoamyl Alcohol 25:24:1 (ThermoFisher Scientific), precipitated and washed with 100% ethanol. DNA was resuspended in 150 microliters of water followed by the addition of 75 microliters of AMPure XP beads (Beckmann Agencourt). Beads were mixed and incubated for 5 minutes, added to a magnet for 2 minutes and the supernatant was collected as size selected fragments. The DNA was precipitated by adding 700 microliters of ethanol and 1 ul of 20 mg/ml glycogen and spun at 16000xg for 10 minutes. The pellet was washed with 70% ethanol and resuspended in 20 microliters of 10mM Tris-HCl, 1mM EDTA. Libraries were prepared using the Swift Biosciences Accel-NGS 2S Plus DNA Library kit according to manufacturer's instructions. Libraries were PCR amplified for 12 cycles according to the manufacturer's instructions. NextSeq 500 SRX13126422 GSM5688964_r1 SRP345841 PRJNA780001 SRS11061298 GSM5688964 GSM5688964 OTHER GENOMIC other CUT&RUN was performed as described by Skene et al 2017). 300,000 cells per sample were isolated and anti-V5 antibody (Invitrogen) was used for all samples. pAG-Mnase was added to each sample to a final concentration of 700ng/ml. Chromatin digestion was performed after addition of CaCl2 and DNA digestion was halted Digestion was allowed to proceed on ice for 30 minutes and halted by the addition of 2X Stop Buffer (340mM NaCl, 20mM EDTA, 4mM EGTA, 50 micrograms/ml RNase A, 50 micrograms/ml glycogen). DNA was extracted by the addition of SDS (final concentration 0.1%) and proteinase K (final 10 micrograms/ml) and incubating at 55 degrees for 1 hour. The material was extracted with one equivalent volume of Phenol/Chloroform/Isoamyl Alcohol 25:24:1 (ThermoFisher Scientific), precipitated and washed with 100% ethanol. DNA was resuspended in 150 microliters of water followed by the addition of 75 microliters of AMPure XP beads (Beckmann Agencourt). Beads were mixed and incubated for 5 minutes, added to a magnet for 2 minutes and the supernatant was collected as size selected fragments. The DNA was precipitated by adding 700 microliters of ethanol and 1 ul of 20 mg/ml glycogen and spun at 16000xg for 10 minutes. The pellet was washed with 70% ethanol and resuspended in 20 microliters of 10mM Tris-HCl, 1mM EDTA. Libraries were prepared using the Swift Biosciences Accel-NGS 2S Plus DNA Library kit according to manufacturer's instructions. Libraries were PCR amplified for 12 cycles according to the manufacturer's instructions. NextSeq 500