SRX18368337 GSM6754693 SRP409536 SRS15854769 GSM6754693 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754693 GSM6754693 GEO Accession GSM6754693 SRX18368338 GSM6754694 SRP409536 SRS15854770 GSM6754694 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754694 GSM6754694 GEO Accession GSM6754694 SRX18368339 GSM6754695 SRP409536 SRS15854771 GSM6754695 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754695 GSM6754695 GEO Accession GSM6754695 SRX18368340 GSM6754696 SRP409536 SRS15854772 GSM6754696 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754696 GSM6754696 GEO Accession GSM6754696 SRX18368341 GSM6754697 SRP409536 SRS15854773 GSM6754697 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754697 GSM6754697 GEO Accession GSM6754697 SRX18368342 GSM6754698 SRP409536 SRS15854774 GSM6754698 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754698 GSM6754698 GEO Accession GSM6754698 SRX18368343 GSM6754699 SRP409536 SRS15854775 GSM6754699 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754699 GSM6754699 GEO Accession GSM6754699 SRX18368344 GSM6754700 SRP409536 SRS15854776 GSM6754700 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754700 GSM6754700 GEO Accession GSM6754700 SRX18368345 GSM6754709 SRP409536 SRS15854777 GSM6754709 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754709 GSM6754709 GEO Accession GSM6754709 SRX18368346 GSM6754710 SRP409536 SRS15854778 GSM6754710 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754710 GSM6754710 GEO Accession GSM6754710 SRX18368347 GSM6754711 SRP409536 SRS15854779 GSM6754711 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754711 GSM6754711 GEO Accession GSM6754711 SRX18368348 GSM6754712 SRP409536 SRS15854780 GSM6754712 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754712 GSM6754712 GEO Accession GSM6754712 SRX18368349 GSM6754713 SRP409536 SRS15854781 GSM6754713 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754713 GSM6754713 GEO Accession GSM6754713 SRX18368350 GSM6754714 SRP409536 SRS15854782 GSM6754714 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754714 GSM6754714 GEO Accession GSM6754714 SRX18368351 GSM6754715 SRP409536 SRS15854784 GSM6754715 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754715 GSM6754715 GEO Accession GSM6754715 SRX18368352 GSM6754716 SRP409536 SRS15854783 GSM6754716 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754716 GSM6754716 GEO Accession GSM6754716 SRX18368353 GSM6754701 SRP409536 SRS15854785 GSM6754701 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754701 GSM6754701 GEO Accession GSM6754701 SRX18368354 GSM6754702 SRP409536 SRS15854786 GSM6754702 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754702 GSM6754702 GEO Accession GSM6754702 SRX18368355 GSM6754703 SRP409536 SRS15854787 GSM6754703 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754703 GSM6754703 GEO Accession GSM6754703 SRX18368356 GSM6754704 SRP409536 SRS15854788 GSM6754704 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754704 GSM6754704 GEO Accession GSM6754704 SRX18368357 GSM6754705 SRP409536 SRS15854789 GSM6754705 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754705 GSM6754705 GEO Accession GSM6754705 SRX18368358 GSM6754706 SRP409536 SRS15854790 GSM6754706 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754706 GSM6754706 GEO Accession GSM6754706 SRX18368359 GSM6754707 SRP409536 SRS15854791 GSM6754707 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754707 GSM6754707 GEO Accession GSM6754707 SRX18368360 GSM6754708 SRP409536 SRS15854792 GSM6754708 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754708 GSM6754708 GEO Accession GSM6754708 SRX18368361 GSM6754717 SRP409536 SRS15854793 GSM6754717 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754717 GSM6754717 GEO Accession GSM6754717 SRX18368362 GSM6754718 SRP409536 SRS15854794 GSM6754718 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754718 GSM6754718 GEO Accession GSM6754718 SRX18368363 GSM6754719 SRP409536 SRS15854795 GSM6754719 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754719 GSM6754719 GEO Accession GSM6754719 SRX18368364 GSM6754720 SRP409536 SRS15854796 GSM6754720 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754720 GSM6754720 GEO Accession GSM6754720 SRX18368365 GSM6754721 SRP409536 SRS15854797 GSM6754721 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754721 GSM6754721 GEO Accession GSM6754721 SRX18368366 GSM6754722 SRP409536 SRS15854798 GSM6754722 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754722 GSM6754722 GEO Accession GSM6754722 SRX18368367 GSM6754723 SRP409536 SRS15854799 GSM6754723 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754723 GSM6754723 GEO Accession GSM6754723 SRX18368368 GSM6754724 SRP409536 SRS15854800 GSM6754724 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754724 GSM6754724 GEO Accession GSM6754724 SRX18368369 GSM6754725 SRP409536 SRS15854801 GSM6754725 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754725 GSM6754725 GEO Accession GSM6754725 SRX18368370 GSM6754726 SRP409536 SRS15854802 GSM6754726 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754726 GSM6754726 GEO Accession GSM6754726 SRX18368371 GSM6754727 SRP409536 SRS15854803 GSM6754727 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754727 GSM6754727 GEO Accession GSM6754727 SRX18368372 GSM6754728 SRP409536 SRS15854804 GSM6754728 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754728 GSM6754728 GEO Accession GSM6754728 SRX18368373 GSM6754729 SRP409536 SRS15854805 GSM6754729 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754729 GSM6754729 GEO Accession GSM6754729 SRX18368374 GSM6754730 SRP409536 SRS15854806 GSM6754730 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 306754730 GSM6754730 GEO Accession GSM6754730 SRX21050389 GSM7634511 SRP409536 PRJNA904799 SRS18321093 GSM7634511 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. For nuclei isolated from brain tissue, slight modifications were made. We performed CUT&RUN on sorted nuclei as described below with minor modifications. We sorted nuclei into CUT&RUN Wash Buffer and immediately bound nuclei to Concanavalin A beads after returning from sorting. Additionally, we substituted 0.1%, 0.1%, and 0.05% digitonin in the Antibody Buffer, Digi-Wash Buffer, and 2X Stop Buffer with 0.1%, 0.1%, and 0.04% Triton X-100. All other steps were the same. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 307634511 GSM7634511 GEO Accession GSM7634511 SRX21050390 GSM7634512 SRP409536 PRJNA904799 SRS18321095 GSM7634512 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. For nuclei isolated from brain tissue, slight modifications were made. We performed CUT&RUN on sorted nuclei as described below with minor modifications. We sorted nuclei into CUT&RUN Wash Buffer and immediately bound nuclei to Concanavalin A beads after returning from sorting. Additionally, we substituted 0.1%, 0.1%, and 0.05% digitonin in the Antibody Buffer, Digi-Wash Buffer, and 2X Stop Buffer with 0.1%, 0.1%, and 0.04% Triton X-100. All other steps were the same. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 307634512 GSM7634512 GEO Accession GSM7634512 SRX21050391 GSM7634513 SRP409536 PRJNA904799 SRS18321094 GSM7634513 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. For nuclei isolated from brain tissue, slight modifications were made. We performed CUT&RUN on sorted nuclei as described below with minor modifications. We sorted nuclei into CUT&RUN Wash Buffer and immediately bound nuclei to Concanavalin A beads after returning from sorting. Additionally, we substituted 0.1%, 0.1%, and 0.05% digitonin in the Antibody Buffer, Digi-Wash Buffer, and 2X Stop Buffer with 0.1%, 0.1%, and 0.04% Triton X-100. All other steps were the same. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 307634513 GSM7634513 GEO Accession GSM7634513 SRX21050392 GSM7634514 SRP409536 PRJNA904799 SRS18321096 GSM7634514 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. For nuclei isolated from brain tissue, slight modifications were made. We performed CUT&RUN on sorted nuclei as described below with minor modifications. We sorted nuclei into CUT&RUN Wash Buffer and immediately bound nuclei to Concanavalin A beads after returning from sorting. Additionally, we substituted 0.1%, 0.1%, and 0.05% digitonin in the Antibody Buffer, Digi-Wash Buffer, and 2X Stop Buffer with 0.1%, 0.1%, and 0.04% Triton X-100. All other steps were the same. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 307634514 GSM7634514 GEO Accession GSM7634514 SRX21050393 GSM7634515 SRP409536 PRJNA904799 SRS18321097 GSM7634515 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. For nuclei isolated from brain tissue, slight modifications were made. We performed CUT&RUN on sorted nuclei as described below with minor modifications. We sorted nuclei into CUT&RUN Wash Buffer and immediately bound nuclei to Concanavalin A beads after returning from sorting. Additionally, we substituted 0.1%, 0.1%, and 0.05% digitonin in the Antibody Buffer, Digi-Wash Buffer, and 2X Stop Buffer with 0.1%, 0.1%, and 0.04% Triton X-100. All other steps were the same. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 307634515 GSM7634515 GEO Accession GSM7634515 SRX21050394 GSM7634516 SRP409536 PRJNA904799 SRS18321098 GSM7634516 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. For nuclei isolated from brain tissue, slight modifications were made. We performed CUT&RUN on sorted nuclei as described below with minor modifications. We sorted nuclei into CUT&RUN Wash Buffer and immediately bound nuclei to Concanavalin A beads after returning from sorting. Additionally, we substituted 0.1%, 0.1%, and 0.05% digitonin in the Antibody Buffer, Digi-Wash Buffer, and 2X Stop Buffer with 0.1%, 0.1%, and 0.04% Triton X-100. All other steps were the same. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 307634516 GSM7634516 GEO Accession GSM7634516 SRX21050395 GSM7634517 SRP409536 PRJNA904799 SRS18321099 GSM7634517 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. For nuclei isolated from brain tissue, slight modifications were made. We performed CUT&RUN on sorted nuclei as described below with minor modifications. We sorted nuclei into CUT&RUN Wash Buffer and immediately bound nuclei to Concanavalin A beads after returning from sorting. Additionally, we substituted 0.1%, 0.1%, and 0.05% digitonin in the Antibody Buffer, Digi-Wash Buffer, and 2X Stop Buffer with 0.1%, 0.1%, and 0.04% Triton X-100. All other steps were the same. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 307634517 GSM7634517 GEO Accession GSM7634517 SRX21050396 GSM7634518 SRP409536 PRJNA904799 SRS18321100 GSM7634518 OTHER GENOMIC other CUT&RUN was completed as previously described (Epicypher). In brief, iPS cells were harvested and then washed in wash buffer (20 mM Hepes KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermadine, 1 Roche Complete Protease Inhibitor EDTA-free mini tablet per 10 mL) and bound to Concanavalin A beads (BioMagPlus) that had been activated and washed with binding buffer (20 mM Hepes KOH pH 8.0, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The cells were then incubated with the Concanavalin A magnetic beads, primary antibody (either IgG (Sigma I8140) or H3K9me3 (Abcam ab8898), and antibody buffer (digi-wash buffer – 0.1% digitonin in wash buffer – with 2 mM EDTA) overnight at 4 C while rotating. Cells were washed with digi-wash buffer and then incubated in a solution containing protein A-MNase and digi-wash buffer for 10 minutes at room temperature. After incubation, the samples were washed in digi-wash buffer and 100 uL digi-wash buffer was added to the samples which were then placed on ice to chill for five minutes. After chilling, 2 uL of 100 mM CaC was added to activate protein A-MNase chromatin digestion. After 2 hours at 4 C with rotation, 100 uL of 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 50 ug/mL RNase A, 50 ug/mL Glycogen) was added to halt the reaction which was then incubated at 37 C for 30 minutes to release chromatin fragments. Supernatant was collected and DNA was extracted using phenol-chloroform and ethanol precipitation. The resulting DNA was quantified on a Qubit Fluorometer. For nuclei isolated from brain tissue, slight modifications were made. We performed CUT&RUN on sorted nuclei as described below with minor modifications. We sorted nuclei into CUT&RUN Wash Buffer and immediately bound nuclei to Concanavalin A beads after returning from sorting. Additionally, we substituted 0.1%, 0.1%, and 0.05% digitonin in the Antibody Buffer, Digi-Wash Buffer, and 2X Stop Buffer with 0.1%, 0.1%, and 0.04% Triton X-100. All other steps were the same. CUT&RUN libraries were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit (NEB #7103) according to manufacturer's protocol. Size selection of adaptor-ligated libraries was performed using AgenCourt Ampure XP beads (Beckman Coulter, A63881) according to the manufacturer's protocol. Size selection targeted <1 kb fragment size and libraries were amplified using 11 PCR cycles. Input amounts for library preparation using the NEBNext Ultra II DNA Library Prep Kit were 1 ng of purified libraries. Library quality and quantities were assessed using the Agilent DNA 1000 reagent kit (Agilent, 5067–1504) on the Agilent Bioanalyzer 2100 (Agilent, 5067–4626) and Qubit high sensitivity RNA assay kit (Thermo Fisher, Q32852), respectively before sequencing on NextSeq500 (Illumina) NextSeq 500 gds 307634518 GSM7634518 GEO Accession GSM7634518