SRX18035868 GSM6685105_r1 SRP404712 PRJNA894548 SRS15542453 GSM6685105 GSM6685105 OTHER GENOMIC other CUT&RUN protocol and all buffer recipes used were adapted from Skene et. al. (Skene et al., 2018) and performed in 0.2ml tubes. Digitonin concentrations were selected based upon trypan blue permeabilization assessment conducted one day prior to experiment as previously described (Skene et al., 2018). Briefly, 200,000 cells were washed and immobilized on 10uL of activated Concanavalin A-coated magnetic beads per condition. Captured cells were resuspended in 0.2ml of antibody buffer containing primary antibody diluted at 1:100. Tubes were rotated 2 hours at 4°C to promote antibody binding to target protein. Cells were then washed with 0.2ml of digitonin wash buffer and resuspended in 0.2ml of digitonin wash buffer containing pA-MNase (expressed and purified in house) diluted to a final concentration of ~0.8ng/uL. Tubes were rotated 1 hour at 4°C to promote protein A binding to primary antibody. Buffer was discarded and replaced with 150uL of digitonin wash buffer. Tubes were cooled to 0°C for 5 minutes, then supplemented with CaCl2 to promote MNase digestion. After 30 minutes, 150uL of 2X STOP buffer containing chelating agents and heterologous yeast spike-in DNA (kind gift Dr. Steven Henikoff, Fred Hutchinson Cancer Research Center) was added to stop the reaction. Cells were incubated at 37°C for 10 minutes to promote release of soluble chromatin fragments, then centrifuged at 16,000xg for 5 minutes at 4°C to pellet cells. Supernatant containing soluble chromatin fragments was transferred to new tubes for DNA extraction. Phenol chloroform extraction was conducted on fragments bound by transcription factors to capture small fragments that may not be captured by column-based extraction methods. Column-based extraction (QIAgen minElute) was conducted for histone CUT&RUN experiments since minimum fragment sizes from histone CUT&RUN experiments typically exceed minimum ranges for column-based DNA extraction. DNA libraries were prepared by PMGC using either NEBNext Ultra II DNA library kit (New England Biolabs) or ThruPLEX DNA-seq kit (Takara Bio USA) as per manufacturer's instructions. Unique molecular indexes were included with p53 CUT&RUN experiments. Libraries were sequenced to obtain >40M paired-end reads / sample on an Illumina NovaSeq6000. Illumina NovaSeq 6000 SRX18035869 GSM6685106_r1 SRP404712 PRJNA894548 SRS15542454 GSM6685106 GSM6685106 OTHER GENOMIC other CUT&RUN protocol and all buffer recipes used were adapted from Skene et. al. (Skene et al., 2018) and performed in 0.2ml tubes. Digitonin concentrations were selected based upon trypan blue permeabilization assessment conducted one day prior to experiment as previously described (Skene et al., 2018). Briefly, 200,000 cells were washed and immobilized on 10uL of activated Concanavalin A-coated magnetic beads per condition. Captured cells were resuspended in 0.2ml of antibody buffer containing primary antibody diluted at 1:100. Tubes were rotated 2 hours at 4°C to promote antibody binding to target protein. Cells were then washed with 0.2ml of digitonin wash buffer and resuspended in 0.2ml of digitonin wash buffer containing pA-MNase (expressed and purified in house) diluted to a final concentration of ~0.8ng/uL. Tubes were rotated 1 hour at 4°C to promote protein A binding to primary antibody. Buffer was discarded and replaced with 150uL of digitonin wash buffer. Tubes were cooled to 0°C for 5 minutes, then supplemented with CaCl2 to promote MNase digestion. After 30 minutes, 150uL of 2X STOP buffer containing chelating agents and heterologous yeast spike-in DNA (kind gift Dr. Steven Henikoff, Fred Hutchinson Cancer Research Center) was added to stop the reaction. Cells were incubated at 37°C for 10 minutes to promote release of soluble chromatin fragments, then centrifuged at 16,000xg for 5 minutes at 4°C to pellet cells. Supernatant containing soluble chromatin fragments was transferred to new tubes for DNA extraction. Phenol chloroform extraction was conducted on fragments bound by transcription factors to capture small fragments that may not be captured by column-based extraction methods. Column-based extraction (QIAgen minElute) was conducted for histone CUT&RUN experiments since minimum fragment sizes from histone CUT&RUN experiments typically exceed minimum ranges for column-based DNA extraction. DNA libraries were prepared by PMGC using either NEBNext Ultra II DNA library kit (New England Biolabs) or ThruPLEX DNA-seq kit (Takara Bio USA) as per manufacturer's instructions. Unique molecular indexes were included with p53 CUT&RUN experiments. Libraries were sequenced to obtain >40M paired-end reads / sample on an Illumina NovaSeq6000. Illumina NovaSeq 6000 SRX18035870 GSM6685107_r1 SRP404712 PRJNA894548 SRS15542455 GSM6685107 GSM6685107 OTHER GENOMIC other CUT&RUN protocol and all buffer recipes used were adapted from Skene et. al. (Skene et al., 2018) and performed in 0.2ml tubes. Digitonin concentrations were selected based upon trypan blue permeabilization assessment conducted one day prior to experiment as previously described (Skene et al., 2018). Briefly, 200,000 cells were washed and immobilized on 10uL of activated Concanavalin A-coated magnetic beads per condition. Captured cells were resuspended in 0.2ml of antibody buffer containing primary antibody diluted at 1:100. Tubes were rotated 2 hours at 4°C to promote antibody binding to target protein. Cells were then washed with 0.2ml of digitonin wash buffer and resuspended in 0.2ml of digitonin wash buffer containing pA-MNase (expressed and purified in house) diluted to a final concentration of ~0.8ng/uL. Tubes were rotated 1 hour at 4°C to promote protein A binding to primary antibody. Buffer was discarded and replaced with 150uL of digitonin wash buffer. Tubes were cooled to 0°C for 5 minutes, then supplemented with CaCl2 to promote MNase digestion. After 30 minutes, 150uL of 2X STOP buffer containing chelating agents and heterologous yeast spike-in DNA (kind gift Dr. Steven Henikoff, Fred Hutchinson Cancer Research Center) was added to stop the reaction. Cells were incubated at 37°C for 10 minutes to promote release of soluble chromatin fragments, then centrifuged at 16,000xg for 5 minutes at 4°C to pellet cells. Supernatant containing soluble chromatin fragments was transferred to new tubes for DNA extraction. Phenol chloroform extraction was conducted on fragments bound by transcription factors to capture small fragments that may not be captured by column-based extraction methods. Column-based extraction (QIAgen minElute) was conducted for histone CUT&RUN experiments since minimum fragment sizes from histone CUT&RUN experiments typically exceed minimum ranges for column-based DNA extraction. DNA libraries were prepared by PMGC using either NEBNext Ultra II DNA library kit (New England Biolabs) or ThruPLEX DNA-seq kit (Takara Bio USA) as per manufacturer's instructions. Unique molecular indexes were included with p53 CUT&RUN experiments. Libraries were sequenced to obtain >40M paired-end reads / sample on an Illumina NovaSeq6000. Illumina NovaSeq 6000 SRX18035871 GSM6685108_r1 SRP404712 PRJNA894548 SRS15542456 GSM6685108 GSM6685108 OTHER GENOMIC other CUT&RUN protocol and all buffer recipes used were adapted from Skene et. al. (Skene et al., 2018) and performed in 0.2ml tubes. Digitonin concentrations were selected based upon trypan blue permeabilization assessment conducted one day prior to experiment as previously described (Skene et al., 2018). Briefly, 200,000 cells were washed and immobilized on 10uL of activated Concanavalin A-coated magnetic beads per condition. Captured cells were resuspended in 0.2ml of antibody buffer containing primary antibody diluted at 1:100. Tubes were rotated 2 hours at 4°C to promote antibody binding to target protein. Cells were then washed with 0.2ml of digitonin wash buffer and resuspended in 0.2ml of digitonin wash buffer containing pA-MNase (expressed and purified in house) diluted to a final concentration of ~0.8ng/uL. Tubes were rotated 1 hour at 4°C to promote protein A binding to primary antibody. Buffer was discarded and replaced with 150uL of digitonin wash buffer. Tubes were cooled to 0°C for 5 minutes, then supplemented with CaCl2 to promote MNase digestion. After 30 minutes, 150uL of 2X STOP buffer containing chelating agents and heterologous yeast spike-in DNA (kind gift Dr. Steven Henikoff, Fred Hutchinson Cancer Research Center) was added to stop the reaction. Cells were incubated at 37°C for 10 minutes to promote release of soluble chromatin fragments, then centrifuged at 16,000xg for 5 minutes at 4°C to pellet cells. Supernatant containing soluble chromatin fragments was transferred to new tubes for DNA extraction. Phenol chloroform extraction was conducted on fragments bound by transcription factors to capture small fragments that may not be captured by column-based extraction methods. Column-based extraction (QIAgen minElute) was conducted for histone CUT&RUN experiments since minimum fragment sizes from histone CUT&RUN experiments typically exceed minimum ranges for column-based DNA extraction. DNA libraries were prepared by PMGC using either NEBNext Ultra II DNA library kit (New England Biolabs) or ThruPLEX DNA-seq kit (Takara Bio USA) as per manufacturer's instructions. Unique molecular indexes were included with p53 CUT&RUN experiments. Libraries were sequenced to obtain >40M paired-end reads / sample on an Illumina NovaSeq6000. Illumina NovaSeq 6000 SRX18035872 GSM6685109_r1 SRP404712 PRJNA894548 SRS15542457 GSM6685109 GSM6685109 OTHER GENOMIC other CUT&RUN protocol and all buffer recipes used were adapted from Skene et. al. (Skene et al., 2018) and performed in 0.2ml tubes. Digitonin concentrations were selected based upon trypan blue permeabilization assessment conducted one day prior to experiment as previously described (Skene et al., 2018). Briefly, 200,000 cells were washed and immobilized on 10uL of activated Concanavalin A-coated magnetic beads per condition. Captured cells were resuspended in 0.2ml of antibody buffer containing primary antibody diluted at 1:100. Tubes were rotated 2 hours at 4°C to promote antibody binding to target protein. Cells were then washed with 0.2ml of digitonin wash buffer and resuspended in 0.2ml of digitonin wash buffer containing pA-MNase (expressed and purified in house) diluted to a final concentration of ~0.8ng/uL. Tubes were rotated 1 hour at 4°C to promote protein A binding to primary antibody. Buffer was discarded and replaced with 150uL of digitonin wash buffer. Tubes were cooled to 0°C for 5 minutes, then supplemented with CaCl2 to promote MNase digestion. After 30 minutes, 150uL of 2X STOP buffer containing chelating agents and heterologous yeast spike-in DNA (kind gift Dr. Steven Henikoff, Fred Hutchinson Cancer Research Center) was added to stop the reaction. Cells were incubated at 37°C for 10 minutes to promote release of soluble chromatin fragments, then centrifuged at 16,000xg for 5 minutes at 4°C to pellet cells. Supernatant containing soluble chromatin fragments was transferred to new tubes for DNA extraction. Phenol chloroform extraction was conducted on fragments bound by transcription factors to capture small fragments that may not be captured by column-based extraction methods. Column-based extraction (QIAgen minElute) was conducted for histone CUT&RUN experiments since minimum fragment sizes from histone CUT&RUN experiments typically exceed minimum ranges for column-based DNA extraction. DNA libraries were prepared by PMGC using either NEBNext Ultra II DNA library kit (New England Biolabs) or ThruPLEX DNA-seq kit (Takara Bio USA) as per manufacturer's instructions. Unique molecular indexes were included with p53 CUT&RUN experiments. Libraries were sequenced to obtain >40M paired-end reads / sample on an Illumina NovaSeq6000. Illumina NovaSeq 6000 SRX18035873 GSM6685110_r1 SRP404712 PRJNA894548 SRS15542458 GSM6685110 GSM6685110 OTHER GENOMIC other CUT&RUN protocol and all buffer recipes used were adapted from Skene et. al. (Skene et al., 2018) and performed in 0.2ml tubes. Digitonin concentrations were selected based upon trypan blue permeabilization assessment conducted one day prior to experiment as previously described (Skene et al., 2018). Briefly, 200,000 cells were washed and immobilized on 10uL of activated Concanavalin A-coated magnetic beads per condition. Captured cells were resuspended in 0.2ml of antibody buffer containing primary antibody diluted at 1:100. Tubes were rotated 2 hours at 4°C to promote antibody binding to target protein. Cells were then washed with 0.2ml of digitonin wash buffer and resuspended in 0.2ml of digitonin wash buffer containing pA-MNase (expressed and purified in house) diluted to a final concentration of ~0.8ng/uL. Tubes were rotated 1 hour at 4°C to promote protein A binding to primary antibody. Buffer was discarded and replaced with 150uL of digitonin wash buffer. Tubes were cooled to 0°C for 5 minutes, then supplemented with CaCl2 to promote MNase digestion. After 30 minutes, 150uL of 2X STOP buffer containing chelating agents and heterologous yeast spike-in DNA (kind gift Dr. Steven Henikoff, Fred Hutchinson Cancer Research Center) was added to stop the reaction. Cells were incubated at 37°C for 10 minutes to promote release of soluble chromatin fragments, then centrifuged at 16,000xg for 5 minutes at 4°C to pellet cells. Supernatant containing soluble chromatin fragments was transferred to new tubes for DNA extraction. Phenol chloroform extraction was conducted on fragments bound by transcription factors to capture small fragments that may not be captured by column-based extraction methods. Column-based extraction (QIAgen minElute) was conducted for histone CUT&RUN experiments since minimum fragment sizes from histone CUT&RUN experiments typically exceed minimum ranges for column-based DNA extraction. DNA libraries were prepared by PMGC using either NEBNext Ultra II DNA library kit (New England Biolabs) or ThruPLEX DNA-seq kit (Takara Bio USA) as per manufacturer's instructions. Unique molecular indexes were included with p53 CUT&RUN experiments. Libraries were sequenced to obtain >40M paired-end reads / sample on an Illumina NovaSeq6000. Illumina NovaSeq 6000 SRX18035874 GSM6685111_r1 SRP404712 PRJNA894548 SRS15542459 GSM6685111 GSM6685111 OTHER GENOMIC other CUT&RUN protocol and all buffer recipes used were adapted from Skene et. al. (Skene et al., 2018) and performed in 0.2ml tubes. Digitonin concentrations were selected based upon trypan blue permeabilization assessment conducted one day prior to experiment as previously described (Skene et al., 2018). Briefly, 200,000 cells were washed and immobilized on 10uL of activated Concanavalin A-coated magnetic beads per condition. Captured cells were resuspended in 0.2ml of antibody buffer containing primary antibody diluted at 1:100. Tubes were rotated 2 hours at 4°C to promote antibody binding to target protein. Cells were then washed with 0.2ml of digitonin wash buffer and resuspended in 0.2ml of digitonin wash buffer containing pA-MNase (expressed and purified in house) diluted to a final concentration of ~0.8ng/uL. Tubes were rotated 1 hour at 4°C to promote protein A binding to primary antibody. Buffer was discarded and replaced with 150uL of digitonin wash buffer. Tubes were cooled to 0°C for 5 minutes, then supplemented with CaCl2 to promote MNase digestion. After 30 minutes, 150uL of 2X STOP buffer containing chelating agents and heterologous yeast spike-in DNA (kind gift Dr. Steven Henikoff, Fred Hutchinson Cancer Research Center) was added to stop the reaction. Cells were incubated at 37°C for 10 minutes to promote release of soluble chromatin fragments, then centrifuged at 16,000xg for 5 minutes at 4°C to pellet cells. Supernatant containing soluble chromatin fragments was transferred to new tubes for DNA extraction. Phenol chloroform extraction was conducted on fragments bound by transcription factors to capture small fragments that may not be captured by column-based extraction methods. Column-based extraction (QIAgen minElute) was conducted for histone CUT&RUN experiments since minimum fragment sizes from histone CUT&RUN experiments typically exceed minimum ranges for column-based DNA extraction. DNA libraries were prepared by PMGC using either NEBNext Ultra II DNA library kit (New England Biolabs) or ThruPLEX DNA-seq kit (Takara Bio USA) as per manufacturer's instructions. Unique molecular indexes were included with p53 CUT&RUN experiments. Libraries were sequenced to obtain >40M paired-end reads / sample on an Illumina NovaSeq6000. Illumina NovaSeq 6000 SRX18035875 GSM6685112_r1 SRP404712 PRJNA894548 SRS15542460 GSM6685112 GSM6685112 OTHER GENOMIC other CUT&RUN protocol and all buffer recipes used were adapted from Skene et. al. (Skene et al., 2018) and performed in 0.2ml tubes. Digitonin concentrations were selected based upon trypan blue permeabilization assessment conducted one day prior to experiment as previously described (Skene et al., 2018). Briefly, 200,000 cells were washed and immobilized on 10uL of activated Concanavalin A-coated magnetic beads per condition. Captured cells were resuspended in 0.2ml of antibody buffer containing primary antibody diluted at 1:100. Tubes were rotated 2 hours at 4°C to promote antibody binding to target protein. Cells were then washed with 0.2ml of digitonin wash buffer and resuspended in 0.2ml of digitonin wash buffer containing pA-MNase (expressed and purified in house) diluted to a final concentration of ~0.8ng/uL. Tubes were rotated 1 hour at 4°C to promote protein A binding to primary antibody. Buffer was discarded and replaced with 150uL of digitonin wash buffer. Tubes were cooled to 0°C for 5 minutes, then supplemented with CaCl2 to promote MNase digestion. After 30 minutes, 150uL of 2X STOP buffer containing chelating agents and heterologous yeast spike-in DNA (kind gift Dr. Steven Henikoff, Fred Hutchinson Cancer Research Center) was added to stop the reaction. Cells were incubated at 37°C for 10 minutes to promote release of soluble chromatin fragments, then centrifuged at 16,000xg for 5 minutes at 4°C to pellet cells. Supernatant containing soluble chromatin fragments was transferred to new tubes for DNA extraction. Phenol chloroform extraction was conducted on fragments bound by transcription factors to capture small fragments that may not be captured by column-based extraction methods. Column-based extraction (QIAgen minElute) was conducted for histone CUT&RUN experiments since minimum fragment sizes from histone CUT&RUN experiments typically exceed minimum ranges for column-based DNA extraction. DNA libraries were prepared by PMGC using either NEBNext Ultra II DNA library kit (New England Biolabs) or ThruPLEX DNA-seq kit (Takara Bio USA) as per manufacturer's instructions. Unique molecular indexes were included with p53 CUT&RUN experiments. Libraries were sequenced to obtain >40M paired-end reads / sample on an Illumina NovaSeq6000. Illumina NovaSeq 6000 SRX18035876 GSM6685113_r1 SRP404712 PRJNA894548 SRS15542461 GSM6685113 GSM6685113 OTHER GENOMIC other CUT&RUN protocol and all buffer recipes used were adapted from Skene et. al. (Skene et al., 2018) and performed in 0.2ml tubes. Digitonin concentrations were selected based upon trypan blue permeabilization assessment conducted one day prior to experiment as previously described (Skene et al., 2018). Briefly, 200,000 cells were washed and immobilized on 10uL of activated Concanavalin A-coated magnetic beads per condition. Captured cells were resuspended in 0.2ml of antibody buffer containing primary antibody diluted at 1:100. Tubes were rotated 2 hours at 4°C to promote antibody binding to target protein. Cells were then washed with 0.2ml of digitonin wash buffer and resuspended in 0.2ml of digitonin wash buffer containing pA-MNase (expressed and purified in house) diluted to a final concentration of ~0.8ng/uL. Tubes were rotated 1 hour at 4°C to promote protein A binding to primary antibody. Buffer was discarded and replaced with 150uL of digitonin wash buffer. Tubes were cooled to 0°C for 5 minutes, then supplemented with CaCl2 to promote MNase digestion. After 30 minutes, 150uL of 2X STOP buffer containing chelating agents and heterologous yeast spike-in DNA (kind gift Dr. Steven Henikoff, Fred Hutchinson Cancer Research Center) was added to stop the reaction. Cells were incubated at 37°C for 10 minutes to promote release of soluble chromatin fragments, then centrifuged at 16,000xg for 5 minutes at 4°C to pellet cells. Supernatant containing soluble chromatin fragments was transferred to new tubes for DNA extraction. Phenol chloroform extraction was conducted on fragments bound by transcription factors to capture small fragments that may not be captured by column-based extraction methods. Column-based extraction (QIAgen minElute) was conducted for histone CUT&RUN experiments since minimum fragment sizes from histone CUT&RUN experiments typically exceed minimum ranges for column-based DNA extraction. DNA libraries were prepared by PMGC using either NEBNext Ultra II DNA library kit (New England Biolabs) or ThruPLEX DNA-seq kit (Takara Bio USA) as per manufacturer's instructions. Unique molecular indexes were included with p53 CUT&RUN experiments. Libraries were sequenced to obtain >40M paired-end reads / sample on an Illumina NovaSeq6000. Illumina NovaSeq 6000 SRX18035877 GSM6685114_r1 SRP404712 PRJNA894548 SRS15542462 GSM6685114 GSM6685114 OTHER GENOMIC other CUT&RUN protocol and all buffer recipes used were adapted from Skene et. al. (Skene et al., 2018) and performed in 0.2ml tubes. Digitonin concentrations were selected based upon trypan blue permeabilization assessment conducted one day prior to experiment as previously described (Skene et al., 2018). Briefly, 200,000 cells were washed and immobilized on 10uL of activated Concanavalin A-coated magnetic beads per condition. Captured cells were resuspended in 0.2ml of antibody buffer containing primary antibody diluted at 1:100. Tubes were rotated 2 hours at 4°C to promote antibody binding to target protein. Cells were then washed with 0.2ml of digitonin wash buffer and resuspended in 0.2ml of digitonin wash buffer containing pA-MNase (expressed and purified in house) diluted to a final concentration of ~0.8ng/uL. Tubes were rotated 1 hour at 4°C to promote protein A binding to primary antibody. Buffer was discarded and replaced with 150uL of digitonin wash buffer. Tubes were cooled to 0°C for 5 minutes, then supplemented with CaCl2 to promote MNase digestion. After 30 minutes, 150uL of 2X STOP buffer containing chelating agents and heterologous yeast spike-in DNA (kind gift Dr. Steven Henikoff, Fred Hutchinson Cancer Research Center) was added to stop the reaction. Cells were incubated at 37°C for 10 minutes to promote release of soluble chromatin fragments, then centrifuged at 16,000xg for 5 minutes at 4°C to pellet cells. Supernatant containing soluble chromatin fragments was transferred to new tubes for DNA extraction. Phenol chloroform extraction was conducted on fragments bound by transcription factors to capture small fragments that may not be captured by column-based extraction methods. Column-based extraction (QIAgen minElute) was conducted for histone CUT&RUN experiments since minimum fragment sizes from histone CUT&RUN experiments typically exceed minimum ranges for column-based DNA extraction. DNA libraries were prepared by PMGC using either NEBNext Ultra II DNA library kit (New England Biolabs) or ThruPLEX DNA-seq kit (Takara Bio USA) as per manufacturer's instructions. Unique molecular indexes were included with p53 CUT&RUN experiments. Libraries were sequenced to obtain >40M paired-end reads / sample on an Illumina NovaSeq6000. Illumina NovaSeq 6000 SRX18035878 GSM6685115_r1 SRP404712 PRJNA894548 SRS15542463 GSM6685115 GSM6685115 OTHER GENOMIC other CUT&RUN protocol and all buffer recipes used were adapted from Skene et. al. (Skene et al., 2018) and performed in 0.2ml tubes. Digitonin concentrations were selected based upon trypan blue permeabilization assessment conducted one day prior to experiment as previously described (Skene et al., 2018). Briefly, 200,000 cells were washed and immobilized on 10uL of activated Concanavalin A-coated magnetic beads per condition. Captured cells were resuspended in 0.2ml of antibody buffer containing primary antibody diluted at 1:100. Tubes were rotated 2 hours at 4°C to promote antibody binding to target protein. Cells were then washed with 0.2ml of digitonin wash buffer and resuspended in 0.2ml of digitonin wash buffer containing pA-MNase (expressed and purified in house) diluted to a final concentration of ~0.8ng/uL. Tubes were rotated 1 hour at 4°C to promote protein A binding to primary antibody. Buffer was discarded and replaced with 150uL of digitonin wash buffer. Tubes were cooled to 0°C for 5 minutes, then supplemented with CaCl2 to promote MNase digestion. After 30 minutes, 150uL of 2X STOP buffer containing chelating agents and heterologous yeast spike-in DNA (kind gift Dr. Steven Henikoff, Fred Hutchinson Cancer Research Center) was added to stop the reaction. Cells were incubated at 37°C for 10 minutes to promote release of soluble chromatin fragments, then centrifuged at 16,000xg for 5 minutes at 4°C to pellet cells. Supernatant containing soluble chromatin fragments was transferred to new tubes for DNA extraction. Phenol chloroform extraction was conducted on fragments bound by transcription factors to capture small fragments that may not be captured by column-based extraction methods. Column-based extraction (QIAgen minElute) was conducted for histone CUT&RUN experiments since minimum fragment sizes from histone CUT&RUN experiments typically exceed minimum ranges for column-based DNA extraction. DNA libraries were prepared by PMGC using either NEBNext Ultra II DNA library kit (New England Biolabs) or ThruPLEX DNA-seq kit (Takara Bio USA) as per manufacturer's instructions. Unique molecular indexes were included with p53 CUT&RUN experiments. Libraries were sequenced to obtain >40M paired-end reads / sample on an Illumina NovaSeq6000. Illumina NovaSeq 6000 SRX18035879 GSM6685116_r1 SRP404712 PRJNA894548 SRS15542464 GSM6685116 GSM6685116 OTHER GENOMIC other CUT&RUN protocol and all buffer recipes used were adapted from Skene et. al. (Skene et al., 2018) and performed in 0.2ml tubes. Digitonin concentrations were selected based upon trypan blue permeabilization assessment conducted one day prior to experiment as previously described (Skene et al., 2018). Briefly, 200,000 cells were washed and immobilized on 10uL of activated Concanavalin A-coated magnetic beads per condition. Captured cells were resuspended in 0.2ml of antibody buffer containing primary antibody diluted at 1:100. Tubes were rotated 2 hours at 4°C to promote antibody binding to target protein. Cells were then washed with 0.2ml of digitonin wash buffer and resuspended in 0.2ml of digitonin wash buffer containing pA-MNase (expressed and purified in house) diluted to a final concentration of ~0.8ng/uL. Tubes were rotated 1 hour at 4°C to promote protein A binding to primary antibody. Buffer was discarded and replaced with 150uL of digitonin wash buffer. Tubes were cooled to 0°C for 5 minutes, then supplemented with CaCl2 to promote MNase digestion. After 30 minutes, 150uL of 2X STOP buffer containing chelating agents and heterologous yeast spike-in DNA (kind gift Dr. Steven Henikoff, Fred Hutchinson Cancer Research Center) was added to stop the reaction. Cells were incubated at 37°C for 10 minutes to promote release of soluble chromatin fragments, then centrifuged at 16,000xg for 5 minutes at 4°C to pellet cells. Supernatant containing soluble chromatin fragments was transferred to new tubes for DNA extraction. Phenol chloroform extraction was conducted on fragments bound by transcription factors to capture small fragments that may not be captured by column-based extraction methods. Column-based extraction (QIAgen minElute) was conducted for histone CUT&RUN experiments since minimum fragment sizes from histone CUT&RUN experiments typically exceed minimum ranges for column-based DNA extraction. DNA libraries were prepared by PMGC using either NEBNext Ultra II DNA library kit (New England Biolabs) or ThruPLEX DNA-seq kit (Takara Bio USA) as per manufacturer's instructions. Unique molecular indexes were included with p53 CUT&RUN experiments. Libraries were sequenced to obtain >40M paired-end reads / sample on an Illumina NovaSeq6000. Illumina NovaSeq 6000 SRX18035880 GSM6685117_r1 SRP404712 PRJNA894548 SRS15542465 GSM6685117 GSM6685117 OTHER GENOMIC other CUT&RUN protocol and all buffer recipes used were adapted from Skene et. al. (Skene et al., 2018) and performed in 0.2ml tubes. Digitonin concentrations were selected based upon trypan blue permeabilization assessment conducted one day prior to experiment as previously described (Skene et al., 2018). Briefly, 200,000 cells were washed and immobilized on 10uL of activated Concanavalin A-coated magnetic beads per condition. Captured cells were resuspended in 0.2ml of antibody buffer containing primary antibody diluted at 1:100. Tubes were rotated 2 hours at 4°C to promote antibody binding to target protein. Cells were then washed with 0.2ml of digitonin wash buffer and resuspended in 0.2ml of digitonin wash buffer containing pA-MNase (expressed and purified in house) diluted to a final concentration of ~0.8ng/uL. Tubes were rotated 1 hour at 4°C to promote protein A binding to primary antibody. Buffer was discarded and replaced with 150uL of digitonin wash buffer. Tubes were cooled to 0°C for 5 minutes, then supplemented with CaCl2 to promote MNase digestion. After 30 minutes, 150uL of 2X STOP buffer containing chelating agents and heterologous yeast spike-in DNA (kind gift Dr. Steven Henikoff, Fred Hutchinson Cancer Research Center) was added to stop the reaction. Cells were incubated at 37°C for 10 minutes to promote release of soluble chromatin fragments, then centrifuged at 16,000xg for 5 minutes at 4°C to pellet cells. Supernatant containing soluble chromatin fragments was transferred to new tubes for DNA extraction. Phenol chloroform extraction was conducted on fragments bound by transcription factors to capture small fragments that may not be captured by column-based extraction methods. Column-based extraction (QIAgen minElute) was conducted for histone CUT&RUN experiments since minimum fragment sizes from histone CUT&RUN experiments typically exceed minimum ranges for column-based DNA extraction. DNA libraries were prepared by PMGC using either NEBNext Ultra II DNA library kit (New England Biolabs) or ThruPLEX DNA-seq kit (Takara Bio USA) as per manufacturer's instructions. Unique molecular indexes were included with p53 CUT&RUN experiments. Libraries were sequenced to obtain >40M paired-end reads / sample on an Illumina NovaSeq6000. Illumina NovaSeq 6000 SRX18035881 GSM6685118_r1 SRP404712 PRJNA894548 SRS15542466 GSM6685118 GSM6685118 OTHER GENOMIC other CUT&RUN protocol and all buffer recipes used were adapted from Skene et. al. (Skene et al., 2018) and performed in 0.2ml tubes. Digitonin concentrations were selected based upon trypan blue permeabilization assessment conducted one day prior to experiment as previously described (Skene et al., 2018). Briefly, 200,000 cells were washed and immobilized on 10uL of activated Concanavalin A-coated magnetic beads per condition. Captured cells were resuspended in 0.2ml of antibody buffer containing primary antibody diluted at 1:100. Tubes were rotated 2 hours at 4°C to promote antibody binding to target protein. Cells were then washed with 0.2ml of digitonin wash buffer and resuspended in 0.2ml of digitonin wash buffer containing pA-MNase (expressed and purified in house) diluted to a final concentration of ~0.8ng/uL. Tubes were rotated 1 hour at 4°C to promote protein A binding to primary antibody. Buffer was discarded and replaced with 150uL of digitonin wash buffer. Tubes were cooled to 0°C for 5 minutes, then supplemented with CaCl2 to promote MNase digestion. After 30 minutes, 150uL of 2X STOP buffer containing chelating agents and heterologous yeast spike-in DNA (kind gift Dr. Steven Henikoff, Fred Hutchinson Cancer Research Center) was added to stop the reaction. Cells were incubated at 37°C for 10 minutes to promote release of soluble chromatin fragments, then centrifuged at 16,000xg for 5 minutes at 4°C to pellet cells. Supernatant containing soluble chromatin fragments was transferred to new tubes for DNA extraction. Phenol chloroform extraction was conducted on fragments bound by transcription factors to capture small fragments that may not be captured by column-based extraction methods. Column-based extraction (QIAgen minElute) was conducted for histone CUT&RUN experiments since minimum fragment sizes from histone CUT&RUN experiments typically exceed minimum ranges for column-based DNA extraction. DNA libraries were prepared by PMGC using either NEBNext Ultra II DNA library kit (New England Biolabs) or ThruPLEX DNA-seq kit (Takara Bio USA) as per manufacturer's instructions. Unique molecular indexes were included with p53 CUT&RUN experiments. Libraries were sequenced to obtain >40M paired-end reads / sample on an Illumina NovaSeq6000. Illumina NovaSeq 6000 SRX18035882 GSM6685119_r1 SRP404712 PRJNA894548 SRS15542467 GSM6685119 GSM6685119 OTHER GENOMIC other CUT&RUN protocol and all buffer recipes used were adapted from Skene et. al. (Skene et al., 2018) and performed in 0.2ml tubes. Digitonin concentrations were selected based upon trypan blue permeabilization assessment conducted one day prior to experiment as previously described (Skene et al., 2018). Briefly, 200,000 cells were washed and immobilized on 10uL of activated Concanavalin A-coated magnetic beads per condition. Captured cells were resuspended in 0.2ml of antibody buffer containing primary antibody diluted at 1:100. Tubes were rotated 2 hours at 4°C to promote antibody binding to target protein. Cells were then washed with 0.2ml of digitonin wash buffer and resuspended in 0.2ml of digitonin wash buffer containing pA-MNase (expressed and purified in house) diluted to a final concentration of ~0.8ng/uL. Tubes were rotated 1 hour at 4°C to promote protein A binding to primary antibody. Buffer was discarded and replaced with 150uL of digitonin wash buffer. Tubes were cooled to 0°C for 5 minutes, then supplemented with CaCl2 to promote MNase digestion. After 30 minutes, 150uL of 2X STOP buffer containing chelating agents and heterologous yeast spike-in DNA (kind gift Dr. Steven Henikoff, Fred Hutchinson Cancer Research Center) was added to stop the reaction. Cells were incubated at 37°C for 10 minutes to promote release of soluble chromatin fragments, then centrifuged at 16,000xg for 5 minutes at 4°C to pellet cells. Supernatant containing soluble chromatin fragments was transferred to new tubes for DNA extraction. Phenol chloroform extraction was conducted on fragments bound by transcription factors to capture small fragments that may not be captured by column-based extraction methods. Column-based extraction (QIAgen minElute) was conducted for histone CUT&RUN experiments since minimum fragment sizes from histone CUT&RUN experiments typically exceed minimum ranges for column-based DNA extraction. DNA libraries were prepared by PMGC using either NEBNext Ultra II DNA library kit (New England Biolabs) or ThruPLEX DNA-seq kit (Takara Bio USA) as per manufacturer's instructions. Unique molecular indexes were included with p53 CUT&RUN experiments. Libraries were sequenced to obtain >40M paired-end reads / sample on an Illumina NovaSeq6000. Illumina NovaSeq 6000 SRX18035883 GSM6685120_r1 SRP404712 PRJNA894548 SRS15542468 GSM6685120 GSM6685120 OTHER GENOMIC other CUT&RUN protocol and all buffer recipes used were adapted from Skene et. al. (Skene et al., 2018) and performed in 0.2ml tubes. Digitonin concentrations were selected based upon trypan blue permeabilization assessment conducted one day prior to experiment as previously described (Skene et al., 2018). Briefly, 200,000 cells were washed and immobilized on 10uL of activated Concanavalin A-coated magnetic beads per condition. Captured cells were resuspended in 0.2ml of antibody buffer containing primary antibody diluted at 1:100. Tubes were rotated 2 hours at 4°C to promote antibody binding to target protein. Cells were then washed with 0.2ml of digitonin wash buffer and resuspended in 0.2ml of digitonin wash buffer containing pA-MNase (expressed and purified in house) diluted to a final concentration of ~0.8ng/uL. Tubes were rotated 1 hour at 4°C to promote protein A binding to primary antibody. Buffer was discarded and replaced with 150uL of digitonin wash buffer. Tubes were cooled to 0°C for 5 minutes, then supplemented with CaCl2 to promote MNase digestion. After 30 minutes, 150uL of 2X STOP buffer containing chelating agents and heterologous yeast spike-in DNA (kind gift Dr. Steven Henikoff, Fred Hutchinson Cancer Research Center) was added to stop the reaction. Cells were incubated at 37°C for 10 minutes to promote release of soluble chromatin fragments, then centrifuged at 16,000xg for 5 minutes at 4°C to pellet cells. Supernatant containing soluble chromatin fragments was transferred to new tubes for DNA extraction. Phenol chloroform extraction was conducted on fragments bound by transcription factors to capture small fragments that may not be captured by column-based extraction methods. Column-based extraction (QIAgen minElute) was conducted for histone CUT&RUN experiments since minimum fragment sizes from histone CUT&RUN experiments typically exceed minimum ranges for column-based DNA extraction. DNA libraries were prepared by PMGC using either NEBNext Ultra II DNA library kit (New England Biolabs) or ThruPLEX DNA-seq kit (Takara Bio USA) as per manufacturer's instructions. Unique molecular indexes were included with p53 CUT&RUN experiments. Libraries were sequenced to obtain >40M paired-end reads / sample on an Illumina NovaSeq6000. Illumina NovaSeq 6000 SRX18035884 GSM6685121_r1 SRP404712 PRJNA894548 SRS15542470 GSM6685121 GSM6685121 OTHER GENOMIC other CUT&RUN protocol and all buffer recipes used were adapted from Skene et. al. (Skene et al., 2018) and performed in 0.2ml tubes. Digitonin concentrations were selected based upon trypan blue permeabilization assessment conducted one day prior to experiment as previously described (Skene et al., 2018). Briefly, 200,000 cells were washed and immobilized on 10uL of activated Concanavalin A-coated magnetic beads per condition. Captured cells were resuspended in 0.2ml of antibody buffer containing primary antibody diluted at 1:100. Tubes were rotated 2 hours at 4°C to promote antibody binding to target protein. Cells were then washed with 0.2ml of digitonin wash buffer and resuspended in 0.2ml of digitonin wash buffer containing pA-MNase (expressed and purified in house) diluted to a final concentration of ~0.8ng/uL. Tubes were rotated 1 hour at 4°C to promote protein A binding to primary antibody. Buffer was discarded and replaced with 150uL of digitonin wash buffer. Tubes were cooled to 0°C for 5 minutes, then supplemented with CaCl2 to promote MNase digestion. After 30 minutes, 150uL of 2X STOP buffer containing chelating agents and heterologous yeast spike-in DNA (kind gift Dr. Steven Henikoff, Fred Hutchinson Cancer Research Center) was added to stop the reaction. Cells were incubated at 37°C for 10 minutes to promote release of soluble chromatin fragments, then centrifuged at 16,000xg for 5 minutes at 4°C to pellet cells. Supernatant containing soluble chromatin fragments was transferred to new tubes for DNA extraction. Phenol chloroform extraction was conducted on fragments bound by transcription factors to capture small fragments that may not be captured by column-based extraction methods. Column-based extraction (QIAgen minElute) was conducted for histone CUT&RUN experiments since minimum fragment sizes from histone CUT&RUN experiments typically exceed minimum ranges for column-based DNA extraction. DNA libraries were prepared by PMGC using either NEBNext Ultra II DNA library kit (New England Biolabs) or ThruPLEX DNA-seq kit (Takara Bio USA) as per manufacturer's instructions. Unique molecular indexes were included with p53 CUT&RUN experiments. Libraries were sequenced to obtain >40M paired-end reads / sample on an Illumina NovaSeq6000. Illumina NovaSeq 6000