SRX18376813 GSM6755625_r1 SRP409739 PRJNA905336 SRS15862885 GSM6755625 GSM6755625 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376814 GSM6755506_r1 SRP409739 PRJNA905336 SRS15862886 GSM6755506 GSM6755506 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376815 GSM6755507_r1 SRP409739 PRJNA905336 SRS15862887 GSM6755507 GSM6755507 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376816 GSM6755508_r1 SRP409739 PRJNA905336 SRS15862888 GSM6755508 GSM6755508 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376817 GSM6755509_r1 SRP409739 PRJNA905336 SRS15862889 GSM6755509 GSM6755509 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376818 GSM6755510_r1 SRP409739 PRJNA905336 SRS15862891 GSM6755510 GSM6755510 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376819 GSM6755511_r1 SRP409739 PRJNA905336 SRS15862890 GSM6755511 GSM6755511 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376820 GSM6755512_r1 SRP409739 PRJNA905336 SRS15862892 GSM6755512 GSM6755512 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376821 GSM6755513_r1 SRP409739 PRJNA905336 SRS15862893 GSM6755513 GSM6755513 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376822 GSM6755554_r1 SRP409739 PRJNA905336 SRS15862894 GSM6755554 GSM6755554 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376823 GSM6755555_r1 SRP409739 PRJNA905336 SRS15862895 GSM6755555 GSM6755555 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376824 GSM6755556_r1 SRP409739 PRJNA905336 SRS15862896 GSM6755556 GSM6755556 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376825 GSM6755557_r1 SRP409739 PRJNA905336 SRS15862897 GSM6755557 GSM6755557 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376826 GSM6755558_r1 SRP409739 PRJNA905336 SRS15862898 GSM6755558 GSM6755558 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376827 GSM6755559_r1 SRP409739 PRJNA905336 SRS15862899 GSM6755559 GSM6755559 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376828 GSM6755560_r1 SRP409739 PRJNA905336 SRS15862900 GSM6755560 GSM6755560 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376829 GSM6755561_r1 SRP409739 PRJNA905336 SRS15862901 GSM6755561 GSM6755561 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376830 GSM6755514_r1 SRP409739 PRJNA905336 SRS15862902 GSM6755514 GSM6755514 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376831 GSM6755515_r1 SRP409739 PRJNA905336 SRS15862903 GSM6755515 GSM6755515 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376832 GSM6755516_r1 SRP409739 PRJNA905336 SRS15862904 GSM6755516 GSM6755516 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376833 GSM6755517_r1 SRP409739 PRJNA905336 SRS15862906 GSM6755517 GSM6755517 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376834 GSM6755518_r1 SRP409739 PRJNA905336 SRS15862905 GSM6755518 GSM6755518 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376835 GSM6755519_r1 SRP409739 PRJNA905336 SRS15862907 GSM6755519 GSM6755519 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376836 GSM6755520_r1 SRP409739 PRJNA905336 SRS15862909 GSM6755520 GSM6755520 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376837 GSM6755521_r1 SRP409739 PRJNA905336 SRS15862908 GSM6755521 GSM6755521 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376838 GSM6755538_r1 SRP409739 PRJNA905336 SRS15862910 GSM6755538 GSM6755538 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376839 GSM6755539_r1 SRP409739 PRJNA905336 SRS15862912 GSM6755539 GSM6755539 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376840 GSM6755540_r1 SRP409739 PRJNA905336 SRS15862911 GSM6755540 GSM6755540 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376841 GSM6755541_r1 SRP409739 PRJNA905336 SRS15862913 GSM6755541 GSM6755541 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376842 GSM6755542_r1 SRP409739 PRJNA905336 SRS15862915 GSM6755542 GSM6755542 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376843 GSM6755543_r1 SRP409739 PRJNA905336 SRS15862914 GSM6755543 GSM6755543 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376844 GSM6755544_r1 SRP409739 PRJNA905336 SRS15862916 GSM6755544 GSM6755544 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376845 GSM6755545_r1 SRP409739 PRJNA905336 SRS15862918 GSM6755545 GSM6755545 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376846 GSM6755562_r1 SRP409739 PRJNA905336 SRS15862917 GSM6755562 GSM6755562 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376847 GSM6755563_r1 SRP409739 PRJNA905336 SRS15862919 GSM6755563 GSM6755563 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376848 GSM6755564_r1 SRP409739 PRJNA905336 SRS15862920 GSM6755564 GSM6755564 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376849 GSM6755565_r1 SRP409739 PRJNA905336 SRS15862921 GSM6755565 GSM6755565 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376850 GSM6755566_r1 SRP409739 PRJNA905336 SRS15862922 GSM6755566 GSM6755566 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376851 GSM6755567_r1 SRP409739 PRJNA905336 SRS15862923 GSM6755567 GSM6755567 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376852 GSM6755568_r1 SRP409739 PRJNA905336 SRS15862924 GSM6755568 GSM6755568 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376853 GSM6755569_r1 SRP409739 PRJNA905336 SRS15862925 GSM6755569 GSM6755569 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376854 GSM6755586_r1 SRP409739 PRJNA905336 SRS15862926 GSM6755586 GSM6755586 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376855 GSM6755587_r1 SRP409739 PRJNA905336 SRS15862927 GSM6755587 GSM6755587 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376856 GSM6755588_r1 SRP409739 PRJNA905336 SRS15862928 GSM6755588 GSM6755588 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376857 GSM6755589_r1 SRP409739 PRJNA905336 SRS15862929 GSM6755589 GSM6755589 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376858 GSM6755590_r1 SRP409739 PRJNA905336 SRS15862930 GSM6755590 GSM6755590 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376859 GSM6755591_r1 SRP409739 PRJNA905336 SRS15862931 GSM6755591 GSM6755591 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376860 GSM6755592_r1 SRP409739 PRJNA905336 SRS15862932 GSM6755592 GSM6755592 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376861 GSM6755593_r1 SRP409739 PRJNA905336 SRS15862933 GSM6755593 GSM6755593 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376862 GSM6755594_r1 SRP409739 PRJNA905336 SRS15862934 GSM6755594 GSM6755594 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376863 GSM6755595_r1 SRP409739 PRJNA905336 SRS15862935 GSM6755595 GSM6755595 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376864 GSM6755596_r1 SRP409739 PRJNA905336 SRS15862936 GSM6755596 GSM6755596 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376865 GSM6755597_r1 SRP409739 PRJNA905336 SRS15862937 GSM6755597 GSM6755597 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376866 GSM6755598_r1 SRP409739 PRJNA905336 SRS15862938 GSM6755598 GSM6755598 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376867 GSM6755599_r1 SRP409739 PRJNA905336 SRS15862939 GSM6755599 GSM6755599 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376868 GSM6755600_r1 SRP409739 PRJNA905336 SRS15862940 GSM6755600 GSM6755600 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376869 GSM6755601_r1 SRP409739 PRJNA905336 SRS15862941 GSM6755601 GSM6755601 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376870 GSM6755626_r1 SRP409739 PRJNA905336 SRS15862942 GSM6755626 GSM6755626 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376871 GSM6755627_r1 SRP409739 PRJNA905336 SRS15862943 GSM6755627 GSM6755627 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376872 GSM6755628_r1 SRP409739 PRJNA905336 SRS15862944 GSM6755628 GSM6755628 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376873 GSM6755629_r1 SRP409739 PRJNA905336 SRS15862945 GSM6755629 GSM6755629 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376874 GSM6755630_r1 SRP409739 PRJNA905336 SRS15862946 GSM6755630 GSM6755630 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376875 GSM6755631_r1 SRP409739 PRJNA905336 SRS15862947 GSM6755631 GSM6755631 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376876 GSM6755632_r1 SRP409739 PRJNA905336 SRS15862948 GSM6755632 GSM6755632 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376877 GSM6755633_r1 SRP409739 PRJNA905336 SRS15862949 GSM6755633 GSM6755633 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376878 GSM6755489_r1 SRP409739 PRJNA905336 SRS15862950 GSM6755489 GSM6755489 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376879 GSM6755498_r1 SRP409739 PRJNA905336 SRS15862951 GSM6755498 GSM6755498 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376880 GSM6755499_r1 SRP409739 PRJNA905336 SRS15862952 GSM6755499 GSM6755499 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376881 GSM6755500_r1 SRP409739 PRJNA905336 SRS15862953 GSM6755500 GSM6755500 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376882 GSM6755501_r1 SRP409739 PRJNA905336 SRS15862954 GSM6755501 GSM6755501 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376883 GSM6755502_r1 SRP409739 PRJNA905336 SRS15862955 GSM6755502 GSM6755502 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376884 GSM6755503_r1 SRP409739 PRJNA905336 SRS15862956 GSM6755503 GSM6755503 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376885 GSM6755504_r1 SRP409739 PRJNA905336 SRS15862957 GSM6755504 GSM6755504 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376886 GSM6755505_r1 SRP409739 PRJNA905336 SRS15862958 GSM6755505 GSM6755505 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376887 GSM6755530_r1 SRP409739 PRJNA905336 SRS15862959 GSM6755530 GSM6755530 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376888 GSM6755531_r1 SRP409739 PRJNA905336 SRS15862960 GSM6755531 GSM6755531 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376889 GSM6755532_r1 SRP409739 PRJNA905336 SRS15862961 GSM6755532 GSM6755532 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376890 GSM6755533_r1 SRP409739 PRJNA905336 SRS15862962 GSM6755533 GSM6755533 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376891 GSM6755534_r1 SRP409739 PRJNA905336 SRS15862963 GSM6755534 GSM6755534 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376892 GSM6755535_r1 SRP409739 PRJNA905336 SRS15862964 GSM6755535 GSM6755535 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376893 GSM6755536_r1 SRP409739 PRJNA905336 SRS15862965 GSM6755536 GSM6755536 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376894 GSM6755537_r1 SRP409739 PRJNA905336 SRS15862966 GSM6755537 GSM6755537 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376895 GSM6755546_r1 SRP409739 PRJNA905336 SRS15862967 GSM6755546 GSM6755546 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376896 GSM6755547_r1 SRP409739 PRJNA905336 SRS15862968 GSM6755547 GSM6755547 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376897 GSM6755548_r1 SRP409739 PRJNA905336 SRS15862969 GSM6755548 GSM6755548 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376898 GSM6755549_r1 SRP409739 PRJNA905336 SRS15862970 GSM6755549 GSM6755549 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376899 GSM6755550_r1 SRP409739 PRJNA905336 SRS15862971 GSM6755550 GSM6755550 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376900 GSM6755551_r1 SRP409739 PRJNA905336 SRS15862972 GSM6755551 GSM6755551 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376901 GSM6755552_r1 SRP409739 PRJNA905336 SRS15862973 GSM6755552 GSM6755552 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376902 GSM6755553_r1 SRP409739 PRJNA905336 SRS15862974 GSM6755553 GSM6755553 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376903 GSM6755578_r1 SRP409739 PRJNA905336 SRS15862976 GSM6755578 GSM6755578 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376904 GSM6755579_r1 SRP409739 PRJNA905336 SRS15862975 GSM6755579 GSM6755579 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376905 GSM6755580_r1 SRP409739 PRJNA905336 SRS15862977 GSM6755580 GSM6755580 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376906 GSM6755581_r1 SRP409739 PRJNA905336 SRS15862979 GSM6755581 GSM6755581 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376907 GSM6755582_r1 SRP409739 PRJNA905336 SRS15862978 GSM6755582 GSM6755582 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376908 GSM6755583_r1 SRP409739 PRJNA905336 SRS15862980 GSM6755583 GSM6755583 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376909 GSM6755584_r1 SRP409739 PRJNA905336 SRS15862982 GSM6755584 GSM6755584 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376910 GSM6755585_r1 SRP409739 PRJNA905336 SRS15862981 GSM6755585 GSM6755585 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376911 GSM6755610_r1 SRP409739 PRJNA905336 SRS15862983 GSM6755610 GSM6755610 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376912 GSM6755611_r1 SRP409739 PRJNA905336 SRS15862984 GSM6755611 GSM6755611 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376913 GSM6755612_r1 SRP409739 PRJNA905336 SRS15862985 GSM6755612 GSM6755612 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376914 GSM6755613_r1 SRP409739 PRJNA905336 SRS15862987 GSM6755613 GSM6755613 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376915 GSM6755614_r1 SRP409739 PRJNA905336 SRS15862986 GSM6755614 GSM6755614 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376916 GSM6755615_r1 SRP409739 PRJNA905336 SRS15862988 GSM6755615 GSM6755615 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376917 GSM6755616_r1 SRP409739 PRJNA905336 SRS15862989 GSM6755616 GSM6755616 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376918 GSM6755617_r1 SRP409739 PRJNA905336 SRS15862990 GSM6755617 GSM6755617 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376919 GSM6755490_r1 SRP409739 PRJNA905336 SRS15862991 GSM6755490 GSM6755490 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376920 GSM6755491_r1 SRP409739 PRJNA905336 SRS15862992 GSM6755491 GSM6755491 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376921 GSM6755492_r1 SRP409739 PRJNA905336 SRS15862993 GSM6755492 GSM6755492 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376922 GSM6755493_r1 SRP409739 PRJNA905336 SRS15862994 GSM6755493 GSM6755493 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376923 GSM6755494_r1 SRP409739 PRJNA905336 SRS15862995 GSM6755494 GSM6755494 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376924 GSM6755495_r1 SRP409739 PRJNA905336 SRS15862996 GSM6755495 GSM6755495 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376925 GSM6755496_r1 SRP409739 PRJNA905336 SRS15862997 GSM6755496 GSM6755496 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376926 GSM6755497_r1 SRP409739 PRJNA905336 SRS15862998 GSM6755497 GSM6755497 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376927 GSM6755522_r1 SRP409739 PRJNA905336 SRS15862999 GSM6755522 GSM6755522 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376928 GSM6755523_r1 SRP409739 PRJNA905336 SRS15863000 GSM6755523 GSM6755523 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376929 GSM6755524_r1 SRP409739 PRJNA905336 SRS15863002 GSM6755524 GSM6755524 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376930 GSM6755525_r1 SRP409739 PRJNA905336 SRS15863001 GSM6755525 GSM6755525 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376931 GSM6755526_r1 SRP409739 PRJNA905336 SRS15863003 GSM6755526 GSM6755526 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376932 GSM6755527_r1 SRP409739 PRJNA905336 SRS15863004 GSM6755527 GSM6755527 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376933 GSM6755528_r1 SRP409739 PRJNA905336 SRS15863005 GSM6755528 GSM6755528 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376934 GSM6755529_r1 SRP409739 PRJNA905336 SRS15863006 GSM6755529 GSM6755529 OTHER GENOMIC other Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376935 GSM6755570_r1 SRP409739 PRJNA905336 SRS15863007 GSM6755570 GSM6755570 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376936 GSM6755571_r1 SRP409739 PRJNA905336 SRS15863008 GSM6755571 GSM6755571 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376937 GSM6755572_r1 SRP409739 PRJNA905336 SRS15863009 GSM6755572 GSM6755572 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376938 GSM6755573_r1 SRP409739 PRJNA905336 SRS15863010 GSM6755573 GSM6755573 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376939 GSM6755574_r1 SRP409739 PRJNA905336 SRS15863011 GSM6755574 GSM6755574 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376940 GSM6755575_r1 SRP409739 PRJNA905336 SRS15863012 GSM6755575 GSM6755575 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376941 GSM6755576_r1 SRP409739 PRJNA905336 SRS15863013 GSM6755576 GSM6755576 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376942 GSM6755577_r1 SRP409739 PRJNA905336 SRS15863014 GSM6755577 GSM6755577 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376943 GSM6755602_r1 SRP409739 PRJNA905336 SRS15863015 GSM6755602 GSM6755602 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376944 GSM6755603_r1 SRP409739 PRJNA905336 SRS15863016 GSM6755603 GSM6755603 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376945 GSM6755604_r1 SRP409739 PRJNA905336 SRS15863017 GSM6755604 GSM6755604 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376946 GSM6755605_r1 SRP409739 PRJNA905336 SRS15863018 GSM6755605 GSM6755605 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376947 GSM6755606_r1 SRP409739 PRJNA905336 SRS15863019 GSM6755606 GSM6755606 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376948 GSM6755607_r1 SRP409739 PRJNA905336 SRS15863020 GSM6755607 GSM6755607 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376949 GSM6755608_r1 SRP409739 PRJNA905336 SRS15863021 GSM6755608 GSM6755608 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376950 GSM6755609_r1 SRP409739 PRJNA905336 SRS15863022 GSM6755609 GSM6755609 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376951 GSM6755634_r1 SRP409739 PRJNA905336 SRS15863023 GSM6755634 GSM6755634 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376952 GSM6755635_r1 SRP409739 PRJNA905336 SRS15863025 GSM6755635 GSM6755635 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376953 GSM6755636_r1 SRP409739 PRJNA905336 SRS15863024 GSM6755636 GSM6755636 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376954 GSM6755637_r1 SRP409739 PRJNA905336 SRS15863026 GSM6755637 GSM6755637 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376955 GSM6755638_r1 SRP409739 PRJNA905336 SRS15863027 GSM6755638 GSM6755638 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376956 GSM6755639_r1 SRP409739 PRJNA905336 SRS15863028 GSM6755639 GSM6755639 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376957 GSM6755640_r1 SRP409739 PRJNA905336 SRS15863030 GSM6755640 GSM6755640 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376958 GSM6755618_r1 SRP409739 PRJNA905336 SRS15863029 GSM6755618 GSM6755618 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376959 GSM6755619_r1 SRP409739 PRJNA905336 SRS15863031 GSM6755619 GSM6755619 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376960 GSM6755620_r1 SRP409739 PRJNA905336 SRS15863032 GSM6755620 GSM6755620 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376961 GSM6755621_r1 SRP409739 PRJNA905336 SRS15863033 GSM6755621 GSM6755621 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376962 GSM6755622_r1 SRP409739 PRJNA905336 SRS15863034 GSM6755622 GSM6755622 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376963 GSM6755623_r1 SRP409739 PRJNA905336 SRS15863035 GSM6755623 GSM6755623 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000 SRX18376964 GSM6755624_r1 SRP409739 PRJNA905336 SRS15863036 GSM6755624 GSM6755624 ChIP-Seq GENOMIC ChIP Cut&Run-Seq on iMEFs was performed as previously described (Skene et al., 2018). In the case of FL for which a fresh frozen sample was available, ~30 mg of tissue were pulverized in liquid nitrogen, cross-linked with 1% formaldehyde for 8 minutes and treated with 250 mM glycine to stop cross-linking. After 2 washes in PBS, the pellet was incubated successively in two lysis buffers and then suspended in a sonication buffer. Each sample was processed using a Covaris S220 sonicator at peak power 175, duty factor 10 cycle/burst 200, for a duration of 4 minutes. In the case of FL for which only formalin-fixed paraffin-embedded tissue was available, chromatin extraction was performed as described previously (Cejas et al., 2016). 8 sections of 10-µm thickness per sample were deparaffined in xylene 3 times, then progressively rehydrated in ethanol solutions of decreasing concentration. Samples were then incubated at 40°C for 1 hour before treatment for 5 minutes with PK. Reaction was stopped with a Protease inhibitor cocktail. Each sample was then sonicated using Covaris S200 sonicator at peak power 240, duty factor 20, cycle/burst 200, for a duration of 40 minutes. Sonicated samples (~5 µg chromatin/sample) were cleared for 2 h using non-coupled magnetic beads, then further mixed with 5 µL antibody and incubated overnight at 4°C. Complexes were pulled down using Protein A Dynabeads, washed with RIPA buffer and de-cross-linked, and genomic DNA was isolated by standard phenol-chloroform extraction. Cut&Run-Seq libraries were prepared using the Accel-NGS 2S plus DNA library kit (Swift Biosciences) for Illumina barcoded system with 16 cycles for amplification. ChIP-Seq libraries were prepared using the Illumina TruSeq ChIP kit. Both Cut&Run-Seq and ChIP-Seq libraries were sequenced on an Illumina Novaseq 6000 (PE100). Illumina NovaSeq 6000