SRX3886538 GSM3082081 SRP137399 SRS3125311 GSM3082081 ChIP-Seq GENOMIC ChIP After DMSO or 3-IAA treatment, cultures were fixed with formaldehyde (1% final) for 10 minutes at room temperature (RT), then quenched with glycine (125 mM final) for 5 minutes. After washing with PBS, fixed cell pellets were preserved at -80°C. Thawed pellets were later spheroplasted by resuspension in PBS along with 100 μl of 2 mg/mL zymolyase for 5 m at 37°C. All ChIP solutions henceforth were supplemented with a protease inhibitor cocktail. After washing with PBS, spheroplasts were lysed in 150 μL lysis buffer (50 mM Tris pH 8.0, 150 mM NaCl, 10 mM EDTA, 1% SDS) at RT for 5 m. Lysates were then adjusted to 1.5 mL with 1350 μL of dilution buffer (20 mM Tris pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100) and transferred to a Covaris milliTube on ice. Sonication of diluted ChIP lysate was performed in a Covaris S220 sonicator, with parameters of 150 W Peak Power, 40% Duty Cycle, and 200 Cycles/burst, for a time of 180 s. After sonication, samples were centrifuged for 10 m at 21,000 x g and 4°C. The soluble lysate was then transferred to a new tube along with 20 μL of Sigma FLAG beads (M8823) pre-blocked with BSA, and the IP was performed for 1 h at RT. Beads were then washed 3 x 1 mL cold wash buffer (20 mM Tris pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% Triton, 0.1% Nonidet-P40) at RT, with each wash lasting 3 m. For extraction and de-crosslinking, washed beads were resuspended in 250 μL elution buffer (50 mM Tris pH 8.0, 250 mM NaCl, 10 mM EDTA, 1% SDS) with 60 μg proteinase K incubated overnight at 1,000 RPM and 65°C in an Eppendorf ThermoMixer. The next morning, ChIP DNA was extracted with 200 μL phenol/chloroform/isoamyl alcohol, treated with 10 μg RNase A for 20 m at 37C, re-extracted with phenol/chloroform, and precipitated with linear acrylamide in >80% EtOH at -80C overnight. Precipitated DNA was pelleted for 20 m at 4°C and 21,000 x g, washed with RT 75% ethanol, re-spun for 5 m, dried at RT, and finally resuspended in 20 μL low-TE (50 mM Tris, 0.1 mM EDTA). Libraries were constructed using the NEBNext Ultra II Library Prep Kit for Illumina at the Indiana University Center for Genomics and Bioinformatics. NextSeq 500 gds 303082081 GSM3082081 GEO Accession GSM3082081 SRX3886539 GSM3082082 SRP137399 SRS3125312 GSM3082082 ChIP-Seq GENOMIC ChIP After DMSO or 3-IAA treatment, cultures were fixed with formaldehyde (1% final) for 10 minutes at room temperature (RT), then quenched with glycine (125 mM final) for 5 minutes. After washing with PBS, fixed cell pellets were preserved at -80°C. Thawed pellets were later spheroplasted by resuspension in PBS along with 100 μl of 2 mg/mL zymolyase for 5 m at 37°C. All ChIP solutions henceforth were supplemented with a protease inhibitor cocktail. After washing with PBS, spheroplasts were lysed in 150 μL lysis buffer (50 mM Tris pH 8.0, 150 mM NaCl, 10 mM EDTA, 1% SDS) at RT for 5 m. Lysates were then adjusted to 1.5 mL with 1350 μL of dilution buffer (20 mM Tris pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100) and transferred to a Covaris milliTube on ice. Sonication of diluted ChIP lysate was performed in a Covaris S220 sonicator, with parameters of 150 W Peak Power, 40% Duty Cycle, and 200 Cycles/burst, for a time of 180 s. After sonication, samples were centrifuged for 10 m at 21,000 x g and 4°C. The soluble lysate was then transferred to a new tube along with 20 μL of Sigma FLAG beads (M8823) pre-blocked with BSA, and the IP was performed for 1 h at RT. Beads were then washed 3 x 1 mL cold wash buffer (20 mM Tris pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% Triton, 0.1% Nonidet-P40) at RT, with each wash lasting 3 m. For extraction and de-crosslinking, washed beads were resuspended in 250 μL elution buffer (50 mM Tris pH 8.0, 250 mM NaCl, 10 mM EDTA, 1% SDS) with 60 μg proteinase K incubated overnight at 1,000 RPM and 65°C in an Eppendorf ThermoMixer. The next morning, ChIP DNA was extracted with 200 μL phenol/chloroform/isoamyl alcohol, treated with 10 μg RNase A for 20 m at 37C, re-extracted with phenol/chloroform, and precipitated with linear acrylamide in >80% EtOH at -80C overnight. Precipitated DNA was pelleted for 20 m at 4°C and 21,000 x g, washed with RT 75% ethanol, re-spun for 5 m, dried at RT, and finally resuspended in 20 μL low-TE (50 mM Tris, 0.1 mM EDTA). Libraries were constructed using the NEBNext Ultra II Library Prep Kit for Illumina at the Indiana University Center for Genomics and Bioinformatics. NextSeq 500 gds 303082082 GSM3082082 GEO Accession GSM3082082 SRX4212599 GSM3189526 SRP137399 PRJNA448794 SRS3415317 GSM3189526 ChIP-Seq GENOMIC ChIP After DMSO or 3-IAA treatment, cultures were fixed with formaldehyde (1% final) for 10 minutes at room temperature (RT), then quenched with glycine (125 mM final) for 5 minutes. After washing with PBS, fixed cell pellets were preserved at -80°C. Thawed pellets were later spheroplasted by resuspension in PBS along with 100 μl of 2 mg/mL zymolyase for 5 m at 37°C. All ChIP solutions henceforth were supplemented with a protease inhibitor cocktail. After washing with PBS, spheroplasts were lysed in 150 μL lysis buffer (50 mM Tris pH 8.0, 150 mM NaCl, 10 mM EDTA, 1% SDS) at RT for 5 m. Lysates were then adjusted to 1.5 mL with 1350 μL of dilution buffer (20 mM Tris pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100) and transferred to a Covaris milliTube on ice. Sonication of diluted ChIP lysate was performed in a Covaris S220 sonicator, with parameters of 150 W Peak Power, 40% Duty Cycle, and 200 Cycles/burst, for a time of 180 s. After sonication, samples were centrifuged for 10 m at 21,000 x g and 4°C. The soluble lysate was then transferred to a new tube along with 20 μL of Sigma FLAG beads (M8823) pre-blocked with BSA, and the IP was performed for 1 h at RT. Beads were then washed 3 x 1 mL cold wash buffer (20 mM Tris pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% Triton, 0.1% Nonidet-P40) at RT, with each wash lasting 3 m. For extraction and de-crosslinking, washed beads were resuspended in 250 μL elution buffer (50 mM Tris pH 8.0, 250 mM NaCl, 10 mM EDTA, 1% SDS) with 60 μg proteinase K incubated overnight at 1,000 RPM and 65°C in an Eppendorf ThermoMixer. The next morning, ChIP DNA was extracted with 200 μL phenol/chloroform/isoamyl alcohol, treated with 10 μg RNase A for 20 m at 37C, re-extracted with phenol/chloroform, and precipitated with linear acrylamide in >80% EtOH at -80C overnight. Precipitated DNA was pelleted for 20 m at 4°C and 21,000 x g, washed with RT 75% ethanol, re-spun for 5 m, dried at RT, and finally resuspended in 20 μL low-TE (50 mM Tris, 0.1 mM EDTA). Libraries were constructed using the NEBNext Ultra II Library Prep Kit for Illumina at the Indiana University Center for Genomics and Bioinformatics. NextSeq 500 gds 303189526 GSM3189526 GEO Accession GSM3189526 SRX4212600 GSM3189527 SRP137399 PRJNA448794 SRS3415318 GSM3189527 ChIP-Seq GENOMIC ChIP After DMSO or 3-IAA treatment, cultures were fixed with formaldehyde (1% final) for 10 minutes at room temperature (RT), then quenched with glycine (125 mM final) for 5 minutes. After washing with PBS, fixed cell pellets were preserved at -80°C. Thawed pellets were later spheroplasted by resuspension in PBS along with 100 μl of 2 mg/mL zymolyase for 5 m at 37°C. All ChIP solutions henceforth were supplemented with a protease inhibitor cocktail. After washing with PBS, spheroplasts were lysed in 150 μL lysis buffer (50 mM Tris pH 8.0, 150 mM NaCl, 10 mM EDTA, 1% SDS) at RT for 5 m. Lysates were then adjusted to 1.5 mL with 1350 μL of dilution buffer (20 mM Tris pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100) and transferred to a Covaris milliTube on ice. Sonication of diluted ChIP lysate was performed in a Covaris S220 sonicator, with parameters of 150 W Peak Power, 40% Duty Cycle, and 200 Cycles/burst, for a time of 180 s. After sonication, samples were centrifuged for 10 m at 21,000 x g and 4°C. The soluble lysate was then transferred to a new tube along with 20 μL of Sigma FLAG beads (M8823) pre-blocked with BSA, and the IP was performed for 1 h at RT. Beads were then washed 3 x 1 mL cold wash buffer (20 mM Tris pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% Triton, 0.1% Nonidet-P40) at RT, with each wash lasting 3 m. For extraction and de-crosslinking, washed beads were resuspended in 250 μL elution buffer (50 mM Tris pH 8.0, 250 mM NaCl, 10 mM EDTA, 1% SDS) with 60 μg proteinase K incubated overnight at 1,000 RPM and 65°C in an Eppendorf ThermoMixer. The next morning, ChIP DNA was extracted with 200 μL phenol/chloroform/isoamyl alcohol, treated with 10 μg RNase A for 20 m at 37C, re-extracted with phenol/chloroform, and precipitated with linear acrylamide in >80% EtOH at -80C overnight. Precipitated DNA was pelleted for 20 m at 4°C and 21,000 x g, washed with RT 75% ethanol, re-spun for 5 m, dried at RT, and finally resuspended in 20 μL low-TE (50 mM Tris, 0.1 mM EDTA). Libraries were constructed using the NEBNext Ultra II Library Prep Kit for Illumina at the Indiana University Center for Genomics and Bioinformatics. NextSeq 500 gds 303189527 GSM3189527 GEO Accession GSM3189527 SRX4212601 GSM3189528 SRP137399 PRJNA448794 SRS3415321 GSM3189528 OTHER GENOMIC other After DMSO or 3-IAA treatment, cultures were fixed with formaldehyde (1% final) for 10 minutes at room temperature (RT), then quenched with glycine (125 mM final) for 5 minutes. After washing with PBS, fixed cell pellets were preserved at -80°C. Thawed pellets were later spheroplasted by resuspension in PBS along with 100 μl of 2 mg/mL zymolyase for 5 m at 37°C. All ChIP solutions henceforth were supplemented with a protease inhibitor cocktail. After washing with PBS, spheroplasts were lysed in 150 μL lysis buffer (50 mM Tris pH 8.0, 150 mM NaCl, 10 mM EDTA, 1% SDS) at RT for 5 m. Lysates were then adjusted to 1.5 mL with 1350 μL of dilution buffer (20 mM Tris pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100) and transferred to a Covaris milliTube on ice. Sonication of diluted ChIP lysate was performed in a Covaris S220 sonicator, with parameters of 150 W Peak Power, 40% Duty Cycle, and 200 Cycles/burst, for a time of 180 s. After sonication, samples were centrifuged for 10 m at 21,000 x g and 4°C. The soluble lysate was then transferred to a new tube along with 20 μL of Sigma FLAG beads (M8823) pre-blocked with BSA, and the IP was performed for 1 h at RT. Beads were then washed 3 x 1 mL cold wash buffer (20 mM Tris pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% Triton, 0.1% Nonidet-P40) at RT, with each wash lasting 3 m. For extraction and de-crosslinking, washed beads were resuspended in 250 μL elution buffer (50 mM Tris pH 8.0, 250 mM NaCl, 10 mM EDTA, 1% SDS) with 60 μg proteinase K incubated overnight at 1,000 RPM and 65°C in an Eppendorf ThermoMixer. The next morning, ChIP DNA was extracted with 200 μL phenol/chloroform/isoamyl alcohol, treated with 10 μg RNase A for 20 m at 37C, re-extracted with phenol/chloroform, and precipitated with linear acrylamide in >80% EtOH at -80C overnight. Precipitated DNA was pelleted for 20 m at 4°C and 21,000 x g, washed with RT 75% ethanol, re-spun for 5 m, dried at RT, and finally resuspended in 20 μL low-TE (50 mM Tris, 0.1 mM EDTA). Libraries were constructed using the NEBNext Ultra II Library Prep Kit for Illumina at the Indiana University Center for Genomics and Bioinformatics. NextSeq 500 gds 303189528 GSM3189528 GEO Accession GSM3189528 SRX4212602 GSM3189529 SRP137399 PRJNA448794 SRS3415319 GSM3189529 OTHER GENOMIC other After DMSO or 3-IAA treatment, cultures were fixed with formaldehyde (1% final) for 10 minutes at room temperature (RT), then quenched with glycine (125 mM final) for 5 minutes. After washing with PBS, fixed cell pellets were preserved at -80°C. Thawed pellets were later spheroplasted by resuspension in PBS along with 100 μl of 2 mg/mL zymolyase for 5 m at 37°C. All ChIP solutions henceforth were supplemented with a protease inhibitor cocktail. After washing with PBS, spheroplasts were lysed in 150 μL lysis buffer (50 mM Tris pH 8.0, 150 mM NaCl, 10 mM EDTA, 1% SDS) at RT for 5 m. Lysates were then adjusted to 1.5 mL with 1350 μL of dilution buffer (20 mM Tris pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100) and transferred to a Covaris milliTube on ice. Sonication of diluted ChIP lysate was performed in a Covaris S220 sonicator, with parameters of 150 W Peak Power, 40% Duty Cycle, and 200 Cycles/burst, for a time of 180 s. After sonication, samples were centrifuged for 10 m at 21,000 x g and 4°C. The soluble lysate was then transferred to a new tube along with 20 μL of Sigma FLAG beads (M8823) pre-blocked with BSA, and the IP was performed for 1 h at RT. Beads were then washed 3 x 1 mL cold wash buffer (20 mM Tris pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% Triton, 0.1% Nonidet-P40) at RT, with each wash lasting 3 m. For extraction and de-crosslinking, washed beads were resuspended in 250 μL elution buffer (50 mM Tris pH 8.0, 250 mM NaCl, 10 mM EDTA, 1% SDS) with 60 μg proteinase K incubated overnight at 1,000 RPM and 65°C in an Eppendorf ThermoMixer. The next morning, ChIP DNA was extracted with 200 μL phenol/chloroform/isoamyl alcohol, treated with 10 μg RNase A for 20 m at 37C, re-extracted with phenol/chloroform, and precipitated with linear acrylamide in >80% EtOH at -80C overnight. Precipitated DNA was pelleted for 20 m at 4°C and 21,000 x g, washed with RT 75% ethanol, re-spun for 5 m, dried at RT, and finally resuspended in 20 μL low-TE (50 mM Tris, 0.1 mM EDTA). Libraries were constructed using the NEBNext Ultra II Library Prep Kit for Illumina at the Indiana University Center for Genomics and Bioinformatics. NextSeq 500 gds 303189529 GSM3189529 GEO Accession GSM3189529 SRX4212603 GSM3189530 SRP137399 PRJNA448794 SRS3415320 GSM3189530 OTHER GENOMIC other After DMSO or 3-IAA treatment, cultures were fixed with formaldehyde (1% final) for 10 minutes at room temperature (RT), then quenched with glycine (125 mM final) for 5 minutes. After washing with PBS, fixed cell pellets were preserved at -80°C. Thawed pellets were later spheroplasted by resuspension in PBS along with 100 μl of 2 mg/mL zymolyase for 5 m at 37°C. All ChIP solutions henceforth were supplemented with a protease inhibitor cocktail. After washing with PBS, spheroplasts were lysed in 150 μL lysis buffer (50 mM Tris pH 8.0, 150 mM NaCl, 10 mM EDTA, 1% SDS) at RT for 5 m. Lysates were then adjusted to 1.5 mL with 1350 μL of dilution buffer (20 mM Tris pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100) and transferred to a Covaris milliTube on ice. Sonication of diluted ChIP lysate was performed in a Covaris S220 sonicator, with parameters of 150 W Peak Power, 40% Duty Cycle, and 200 Cycles/burst, for a time of 180 s. After sonication, samples were centrifuged for 10 m at 21,000 x g and 4°C. The soluble lysate was then transferred to a new tube along with 20 μL of Sigma FLAG beads (M8823) pre-blocked with BSA, and the IP was performed for 1 h at RT. Beads were then washed 3 x 1 mL cold wash buffer (20 mM Tris pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% Triton, 0.1% Nonidet-P40) at RT, with each wash lasting 3 m. For extraction and de-crosslinking, washed beads were resuspended in 250 μL elution buffer (50 mM Tris pH 8.0, 250 mM NaCl, 10 mM EDTA, 1% SDS) with 60 μg proteinase K incubated overnight at 1,000 RPM and 65°C in an Eppendorf ThermoMixer. The next morning, ChIP DNA was extracted with 200 μL phenol/chloroform/isoamyl alcohol, treated with 10 μg RNase A for 20 m at 37C, re-extracted with phenol/chloroform, and precipitated with linear acrylamide in >80% EtOH at -80C overnight. Precipitated DNA was pelleted for 20 m at 4°C and 21,000 x g, washed with RT 75% ethanol, re-spun for 5 m, dried at RT, and finally resuspended in 20 μL low-TE (50 mM Tris, 0.1 mM EDTA). Libraries were constructed using the NEBNext Ultra II Library Prep Kit for Illumina at the Indiana University Center for Genomics and Bioinformatics. NextSeq 500 gds 303189530 GSM3189530 GEO Accession GSM3189530