SRX1494706 GSM1977385 SRP067656 SRS1217485 GSM1977385 ChIP-Seq GENOMIC ChIP Samples were ground to a fine powder in liquid nitrogen. For chromatin preparation, powder was resuspended in lysis buffer (50mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 5 mM benzamidine, 2 mM PMSF, 1 X Roche complete EDTA free protease inhibitors) and further treated by sonication to lyse the remaining cells using a microtip sonifier (Branson). Chromatin was then sheared in a bioruptor sonication bath (Diagenode) for 10 cycles (30s on / 30s off) at high power setting. An aliquot was saved to serve as input control and the rest of the chromatin solution was incubated with ChIP grade Protein A/G magnetic beads (Life technologies) coupled to a monoclonal anti-HA antibody (Sigma) for 10h at 4°C. Beads were washed three times in lysis buffer, two times in high salt buffer (50 mM HEPES pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 1 X Roche complete EDTA free protease inhibitors) and once in TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 7.5). DNA / Ros1HA complexes were eluted from the beads in TE SDS buffer (10 mM Tris-HCl, 1 mM EDTA, 1% SDS, pH 7.5) by incubation for15 min at 65°C. Samples and input controls were de-crosslinked for 8-10h at 65°C in TE SDS buffer containing 200 mM NaCl and 0.65 µg/µL proteinase K. DNA was purified using the ChIP DNA clean and concentrator kit (Zymo research). The experiment was done in three biological replicates which were sequenced separately. DNA libraries were prepared using the Illumina TruSeq RNA sample preparation Kit v2 starting from the end repair step of the protocol. Up to 100 ng ChIP DNA was used as starting material. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified for 18 PCR cycles to create the final libraries. After validation (Agilent 2200 TapeStation) and quantification using the KAPA Library Quantification Kit (VWR, Erlangen, Germany) and the Applied Biosystems 7900HT Sequence Detection System, equimolar amounts of library were pooled. The pool was sequenced using the Illumina TruSeq PE Cluster Kit v3 and the Illumina TruSeq SBS Kit v3-HS (101x7x101 Cycles) on an Illumina HiSeq 2000 sequencer with a paired-end (101x7x101 cycles) protocol. Illumina HiSeq 2000 gds 301977385 GEO Accession GSM1977385 SRX1494707 GSM1977386 SRP067656 SRS1217484 GSM1977386 ChIP-Seq GENOMIC ChIP Samples were ground to a fine powder in liquid nitrogen. For chromatin preparation, powder was resuspended in lysis buffer (50mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 5 mM benzamidine, 2 mM PMSF, 1 X Roche complete EDTA free protease inhibitors) and further treated by sonication to lyse the remaining cells using a microtip sonifier (Branson). Chromatin was then sheared in a bioruptor sonication bath (Diagenode) for 10 cycles (30s on / 30s off) at high power setting. An aliquot was saved to serve as input control and the rest of the chromatin solution was incubated with ChIP grade Protein A/G magnetic beads (Life technologies) coupled to a monoclonal anti-HA antibody (Sigma) for 10h at 4°C. Beads were washed three times in lysis buffer, two times in high salt buffer (50 mM HEPES pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 1 X Roche complete EDTA free protease inhibitors) and once in TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 7.5). DNA / Ros1HA complexes were eluted from the beads in TE SDS buffer (10 mM Tris-HCl, 1 mM EDTA, 1% SDS, pH 7.5) by incubation for15 min at 65°C. Samples and input controls were de-crosslinked for 8-10h at 65°C in TE SDS buffer containing 200 mM NaCl and 0.65 µg/µL proteinase K. DNA was purified using the ChIP DNA clean and concentrator kit (Zymo research). The experiment was done in three biological replicates which were sequenced separately. DNA libraries were prepared using the Illumina TruSeq RNA sample preparation Kit v2 starting from the end repair step of the protocol. Up to 100 ng ChIP DNA was used as starting material. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified for 18 PCR cycles to create the final libraries. After validation (Agilent 2200 TapeStation) and quantification using the KAPA Library Quantification Kit (VWR, Erlangen, Germany) and the Applied Biosystems 7900HT Sequence Detection System, equimolar amounts of library were pooled. The pool was sequenced using the Illumina TruSeq PE Cluster Kit v3 and the Illumina TruSeq SBS Kit v3-HS (101x7x101 Cycles) on an Illumina HiSeq 2000 sequencer with a paired-end (101x7x101 cycles) protocol. Illumina HiSeq 2000 gds 301977386 GEO Accession GSM1977386 SRX1494708 GSM1977387 SRP067656 SRS1217483 GSM1977387 ChIP-Seq GENOMIC ChIP Samples were ground to a fine powder in liquid nitrogen. For chromatin preparation, powder was resuspended in lysis buffer (50mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 5 mM benzamidine, 2 mM PMSF, 1 X Roche complete EDTA free protease inhibitors) and further treated by sonication to lyse the remaining cells using a microtip sonifier (Branson). Chromatin was then sheared in a bioruptor sonication bath (Diagenode) for 10 cycles (30s on / 30s off) at high power setting. An aliquot was saved to serve as input control and the rest of the chromatin solution was incubated with ChIP grade Protein A/G magnetic beads (Life technologies) coupled to a monoclonal anti-HA antibody (Sigma) for 10h at 4°C. Beads were washed three times in lysis buffer, two times in high salt buffer (50 mM HEPES pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 1 X Roche complete EDTA free protease inhibitors) and once in TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 7.5). DNA / Ros1HA complexes were eluted from the beads in TE SDS buffer (10 mM Tris-HCl, 1 mM EDTA, 1% SDS, pH 7.5) by incubation for15 min at 65°C. Samples and input controls were de-crosslinked for 8-10h at 65°C in TE SDS buffer containing 200 mM NaCl and 0.65 µg/µL proteinase K. DNA was purified using the ChIP DNA clean and concentrator kit (Zymo research). The experiment was done in three biological replicates which were sequenced separately. DNA libraries were prepared using the Illumina TruSeq RNA sample preparation Kit v2 starting from the end repair step of the protocol. Up to 100 ng ChIP DNA was used as starting material. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified for 18 PCR cycles to create the final libraries. After validation (Agilent 2200 TapeStation) and quantification using the KAPA Library Quantification Kit (VWR, Erlangen, Germany) and the Applied Biosystems 7900HT Sequence Detection System, equimolar amounts of library were pooled. The pool was sequenced using the Illumina TruSeq PE Cluster Kit v3 and the Illumina TruSeq SBS Kit v3-HS (101x7x101 Cycles) on an Illumina HiSeq 2000 sequencer with a paired-end (101x7x101 cycles) protocol. Illumina HiSeq 2000 gds 301977387 GEO Accession GSM1977387 SRX1494709 GSM1977388 SRP067656 SRS1217481 GSM1977388 ChIP-Seq GENOMIC ChIP Samples were ground to a fine powder in liquid nitrogen. For chromatin preparation, powder was resuspended in lysis buffer (50mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 5 mM benzamidine, 2 mM PMSF, 1 X Roche complete EDTA free protease inhibitors) and further treated by sonication to lyse the remaining cells using a microtip sonifier (Branson). Chromatin was then sheared in a bioruptor sonication bath (Diagenode) for 10 cycles (30s on / 30s off) at high power setting. An aliquot was saved to serve as input control and the rest of the chromatin solution was incubated with ChIP grade Protein A/G magnetic beads (Life technologies) coupled to a monoclonal anti-HA antibody (Sigma) for 10h at 4°C. Beads were washed three times in lysis buffer, two times in high salt buffer (50 mM HEPES pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 1 X Roche complete EDTA free protease inhibitors) and once in TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 7.5). DNA / Ros1HA complexes were eluted from the beads in TE SDS buffer (10 mM Tris-HCl, 1 mM EDTA, 1% SDS, pH 7.5) by incubation for15 min at 65°C. Samples and input controls were de-crosslinked for 8-10h at 65°C in TE SDS buffer containing 200 mM NaCl and 0.65 µg/µL proteinase K. DNA was purified using the ChIP DNA clean and concentrator kit (Zymo research). The experiment was done in three biological replicates which were sequenced separately. DNA libraries were prepared using the Illumina TruSeq RNA sample preparation Kit v2 starting from the end repair step of the protocol. Up to 100 ng ChIP DNA was used as starting material. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified for 18 PCR cycles to create the final libraries. After validation (Agilent 2200 TapeStation) and quantification using the KAPA Library Quantification Kit (VWR, Erlangen, Germany) and the Applied Biosystems 7900HT Sequence Detection System, equimolar amounts of library were pooled. The pool was sequenced using the Illumina TruSeq PE Cluster Kit v3 and the Illumina TruSeq SBS Kit v3-HS (101x7x101 Cycles) on an Illumina HiSeq 2000 sequencer with a paired-end (101x7x101 cycles) protocol. Illumina HiSeq 2000 gds 301977388 GEO Accession GSM1977388 SRX1494710 GSM1977389 SRP067656 SRS1217482 GSM1977389 ChIP-Seq GENOMIC ChIP Samples were ground to a fine powder in liquid nitrogen. For chromatin preparation, powder was resuspended in lysis buffer (50mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 5 mM benzamidine, 2 mM PMSF, 1 X Roche complete EDTA free protease inhibitors) and further treated by sonication to lyse the remaining cells using a microtip sonifier (Branson). Chromatin was then sheared in a bioruptor sonication bath (Diagenode) for 10 cycles (30s on / 30s off) at high power setting. An aliquot was saved to serve as input control and the rest of the chromatin solution was incubated with ChIP grade Protein A/G magnetic beads (Life technologies) coupled to a monoclonal anti-HA antibody (Sigma) for 10h at 4°C. Beads were washed three times in lysis buffer, two times in high salt buffer (50 mM HEPES pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 1 X Roche complete EDTA free protease inhibitors) and once in TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 7.5). DNA / Ros1HA complexes were eluted from the beads in TE SDS buffer (10 mM Tris-HCl, 1 mM EDTA, 1% SDS, pH 7.5) by incubation for15 min at 65°C. Samples and input controls were de-crosslinked for 8-10h at 65°C in TE SDS buffer containing 200 mM NaCl and 0.65 µg/µL proteinase K. DNA was purified using the ChIP DNA clean and concentrator kit (Zymo research). The experiment was done in three biological replicates which were sequenced separately. DNA libraries were prepared using the Illumina TruSeq RNA sample preparation Kit v2 starting from the end repair step of the protocol. Up to 100 ng ChIP DNA was used as starting material. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified for 18 PCR cycles to create the final libraries. After validation (Agilent 2200 TapeStation) and quantification using the KAPA Library Quantification Kit (VWR, Erlangen, Germany) and the Applied Biosystems 7900HT Sequence Detection System, equimolar amounts of library were pooled. The pool was sequenced using the Illumina TruSeq PE Cluster Kit v3 and the Illumina TruSeq SBS Kit v3-HS (101x7x101 Cycles) on an Illumina HiSeq 2000 sequencer with a paired-end (101x7x101 cycles) protocol. Illumina HiSeq 2000 gds 301977389 GEO Accession GSM1977389 SRX1494711 GSM1977390 SRP067656 SRS1217480 GSM1977390 ChIP-Seq GENOMIC ChIP Samples were ground to a fine powder in liquid nitrogen. For chromatin preparation, powder was resuspended in lysis buffer (50mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 5 mM benzamidine, 2 mM PMSF, 1 X Roche complete EDTA free protease inhibitors) and further treated by sonication to lyse the remaining cells using a microtip sonifier (Branson). Chromatin was then sheared in a bioruptor sonication bath (Diagenode) for 10 cycles (30s on / 30s off) at high power setting. An aliquot was saved to serve as input control and the rest of the chromatin solution was incubated with ChIP grade Protein A/G magnetic beads (Life technologies) coupled to a monoclonal anti-HA antibody (Sigma) for 10h at 4°C. Beads were washed three times in lysis buffer, two times in high salt buffer (50 mM HEPES pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 1 X Roche complete EDTA free protease inhibitors) and once in TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 7.5). DNA / Ros1HA complexes were eluted from the beads in TE SDS buffer (10 mM Tris-HCl, 1 mM EDTA, 1% SDS, pH 7.5) by incubation for15 min at 65°C. Samples and input controls were de-crosslinked for 8-10h at 65°C in TE SDS buffer containing 200 mM NaCl and 0.65 µg/µL proteinase K. DNA was purified using the ChIP DNA clean and concentrator kit (Zymo research). The experiment was done in three biological replicates which were sequenced separately. DNA libraries were prepared using the Illumina TruSeq RNA sample preparation Kit v2 starting from the end repair step of the protocol. Up to 100 ng ChIP DNA was used as starting material. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified for 18 PCR cycles to create the final libraries. After validation (Agilent 2200 TapeStation) and quantification using the KAPA Library Quantification Kit (VWR, Erlangen, Germany) and the Applied Biosystems 7900HT Sequence Detection System, equimolar amounts of library were pooled. The pool was sequenced using the Illumina TruSeq PE Cluster Kit v3 and the Illumina TruSeq SBS Kit v3-HS (101x7x101 Cycles) on an Illumina HiSeq 2000 sequencer with a paired-end (101x7x101 cycles) protocol. Illumina HiSeq 2000 gds 301977390 GEO Accession GSM1977390 SRX1494712 GSM1977391 SRP067656 SRS1217479 GSM1977391 ChIP-Seq GENOMIC ChIP Samples were ground to a fine powder in liquid nitrogen. For chromatin preparation, powder was resuspended in lysis buffer (50mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 5 mM benzamidine, 2 mM PMSF, 1 X Roche complete EDTA free protease inhibitors) and further treated by sonication to lyse the remaining cells using a microtip sonifier (Branson). Chromatin was then sheared in a bioruptor sonication bath (Diagenode) for 10 cycles (30s on / 30s off) at high power setting. An aliquot was saved to serve as input control and the rest of the chromatin solution was incubated with ChIP grade Protein A/G magnetic beads (Life technologies) coupled to a monoclonal anti-HA antibody (Sigma) for 10h at 4°C. Beads were washed three times in lysis buffer, two times in high salt buffer (50 mM HEPES pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 1 X Roche complete EDTA free protease inhibitors) and once in TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 7.5). DNA / Ros1HA complexes were eluted from the beads in TE SDS buffer (10 mM Tris-HCl, 1 mM EDTA, 1% SDS, pH 7.5) by incubation for15 min at 65°C. Samples and input controls were de-crosslinked for 8-10h at 65°C in TE SDS buffer containing 200 mM NaCl and 0.65 µg/µL proteinase K. DNA was purified using the ChIP DNA clean and concentrator kit (Zymo research). The experiment was done in three biological replicates which were sequenced separately. DNA libraries were prepared using the Illumina TruSeq RNA sample preparation Kit v2 starting from the end repair step of the protocol. Up to 100 ng ChIP DNA was used as starting material. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified for 18 PCR cycles to create the final libraries. After validation (Agilent 2200 TapeStation) and quantification using the KAPA Library Quantification Kit (VWR, Erlangen, Germany) and the Applied Biosystems 7900HT Sequence Detection System, equimolar amounts of library were pooled. The pool was sequenced using the Illumina TruSeq PE Cluster Kit v3 and the Illumina TruSeq SBS Kit v3-HS (101x7x101 Cycles) on an Illumina HiSeq 2000 sequencer with a paired-end (101x7x101 cycles) protocol. Illumina HiSeq 2000 gds 301977391 GEO Accession GSM1977391 SRX1494713 GSM1977392 SRP067656 SRS1217478 GSM1977392 ChIP-Seq GENOMIC ChIP Samples were ground to a fine powder in liquid nitrogen. For chromatin preparation, powder was resuspended in lysis buffer (50mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 5 mM benzamidine, 2 mM PMSF, 1 X Roche complete EDTA free protease inhibitors) and further treated by sonication to lyse the remaining cells using a microtip sonifier (Branson). Chromatin was then sheared in a bioruptor sonication bath (Diagenode) for 10 cycles (30s on / 30s off) at high power setting. An aliquot was saved to serve as input control and the rest of the chromatin solution was incubated with ChIP grade Protein A/G magnetic beads (Life technologies) coupled to a monoclonal anti-HA antibody (Sigma) for 10h at 4°C. Beads were washed three times in lysis buffer, two times in high salt buffer (50 mM HEPES pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 1 X Roche complete EDTA free protease inhibitors) and once in TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 7.5). DNA / Ros1HA complexes were eluted from the beads in TE SDS buffer (10 mM Tris-HCl, 1 mM EDTA, 1% SDS, pH 7.5) by incubation for15 min at 65°C. Samples and input controls were de-crosslinked for 8-10h at 65°C in TE SDS buffer containing 200 mM NaCl and 0.65 µg/µL proteinase K. DNA was purified using the ChIP DNA clean and concentrator kit (Zymo research). The experiment was done in three biological replicates which were sequenced separately. DNA libraries were prepared using the Illumina TruSeq RNA sample preparation Kit v2 starting from the end repair step of the protocol. Up to 100 ng ChIP DNA was used as starting material. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified for 18 PCR cycles to create the final libraries. After validation (Agilent 2200 TapeStation) and quantification using the KAPA Library Quantification Kit (VWR, Erlangen, Germany) and the Applied Biosystems 7900HT Sequence Detection System, equimolar amounts of library were pooled. The pool was sequenced using the Illumina TruSeq PE Cluster Kit v3 and the Illumina TruSeq SBS Kit v3-HS (101x7x101 Cycles) on an Illumina HiSeq 2000 sequencer with a paired-end (101x7x101 cycles) protocol. Illumina HiSeq 2000 gds 301977392 GEO Accession GSM1977392 SRX1494714 GSM1977393 SRP067656 SRS1217477 GSM1977393 ChIP-Seq GENOMIC ChIP Samples were ground to a fine powder in liquid nitrogen. For chromatin preparation, powder was resuspended in lysis buffer (50mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 5 mM benzamidine, 2 mM PMSF, 1 X Roche complete EDTA free protease inhibitors) and further treated by sonication to lyse the remaining cells using a microtip sonifier (Branson). Chromatin was then sheared in a bioruptor sonication bath (Diagenode) for 10 cycles (30s on / 30s off) at high power setting. An aliquot was saved to serve as input control and the rest of the chromatin solution was incubated with ChIP grade Protein A/G magnetic beads (Life technologies) coupled to a monoclonal anti-HA antibody (Sigma) for 10h at 4°C. Beads were washed three times in lysis buffer, two times in high salt buffer (50 mM HEPES pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 1 X Roche complete EDTA free protease inhibitors) and once in TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 7.5). DNA / Ros1HA complexes were eluted from the beads in TE SDS buffer (10 mM Tris-HCl, 1 mM EDTA, 1% SDS, pH 7.5) by incubation for15 min at 65°C. Samples and input controls were de-crosslinked for 8-10h at 65°C in TE SDS buffer containing 200 mM NaCl and 0.65 µg/µL proteinase K. DNA was purified using the ChIP DNA clean and concentrator kit (Zymo research). The experiment was done in three biological replicates which were sequenced separately. DNA libraries were prepared using the Illumina TruSeq RNA sample preparation Kit v2 starting from the end repair step of the protocol. Up to 100 ng ChIP DNA was used as starting material. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified for 18 PCR cycles to create the final libraries. After validation (Agilent 2200 TapeStation) and quantification using the KAPA Library Quantification Kit (VWR, Erlangen, Germany) and the Applied Biosystems 7900HT Sequence Detection System, equimolar amounts of library were pooled. The pool was sequenced using the Illumina TruSeq PE Cluster Kit v3 and the Illumina TruSeq SBS Kit v3-HS (101x7x101 Cycles) on an Illumina HiSeq 2000 sequencer with a paired-end (101x7x101 cycles) protocol. Illumina HiSeq 2000 gds 301977393 GEO Accession GSM1977393 SRX1494715 GSM1977394 SRP067656 SRS1217476 GSM1977394 ChIP-Seq GENOMIC ChIP Samples were ground to a fine powder in liquid nitrogen. For chromatin preparation, powder was resuspended in lysis buffer (50mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 5 mM benzamidine, 2 mM PMSF, 1 X Roche complete EDTA free protease inhibitors) and further treated by sonication to lyse the remaining cells using a microtip sonifier (Branson). Chromatin was then sheared in a bioruptor sonication bath (Diagenode) for 10 cycles (30s on / 30s off) at high power setting. An aliquot was saved to serve as input control and the rest of the chromatin solution was incubated with ChIP grade Protein A/G magnetic beads (Life technologies) coupled to a monoclonal anti-HA antibody (Sigma) for 10h at 4°C. Beads were washed three times in lysis buffer, two times in high salt buffer (50 mM HEPES pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 1 X Roche complete EDTA free protease inhibitors) and once in TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 7.5). DNA / Ros1HA complexes were eluted from the beads in TE SDS buffer (10 mM Tris-HCl, 1 mM EDTA, 1% SDS, pH 7.5) by incubation for15 min at 65°C. Samples and input controls were de-crosslinked for 8-10h at 65°C in TE SDS buffer containing 200 mM NaCl and 0.65 µg/µL proteinase K. DNA was purified using the ChIP DNA clean and concentrator kit (Zymo research). The experiment was done in three biological replicates which were sequenced separately. DNA libraries were prepared using the Illumina TruSeq RNA sample preparation Kit v2 starting from the end repair step of the protocol. Up to 100 ng ChIP DNA was used as starting material. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified for 18 PCR cycles to create the final libraries. After validation (Agilent 2200 TapeStation) and quantification using the KAPA Library Quantification Kit (VWR, Erlangen, Germany) and the Applied Biosystems 7900HT Sequence Detection System, equimolar amounts of library were pooled. The pool was sequenced using the Illumina TruSeq PE Cluster Kit v3 and the Illumina TruSeq SBS Kit v3-HS (101x7x101 Cycles) on an Illumina HiSeq 2000 sequencer with a paired-end (101x7x101 cycles) protocol. Illumina HiSeq 2000 gds 301977394 GEO Accession GSM1977394 SRX1494716 GSM1977395 SRP067656 SRS1217475 GSM1977395 ChIP-Seq GENOMIC ChIP Samples were ground to a fine powder in liquid nitrogen. For chromatin preparation, powder was resuspended in lysis buffer (50mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 5 mM benzamidine, 2 mM PMSF, 1 X Roche complete EDTA free protease inhibitors) and further treated by sonication to lyse the remaining cells using a microtip sonifier (Branson). Chromatin was then sheared in a bioruptor sonication bath (Diagenode) for 10 cycles (30s on / 30s off) at high power setting. An aliquot was saved to serve as input control and the rest of the chromatin solution was incubated with ChIP grade Protein A/G magnetic beads (Life technologies) coupled to a monoclonal anti-HA antibody (Sigma) for 10h at 4°C. Beads were washed three times in lysis buffer, two times in high salt buffer (50 mM HEPES pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 1 X Roche complete EDTA free protease inhibitors) and once in TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 7.5). DNA / Ros1HA complexes were eluted from the beads in TE SDS buffer (10 mM Tris-HCl, 1 mM EDTA, 1% SDS, pH 7.5) by incubation for15 min at 65°C. Samples and input controls were de-crosslinked for 8-10h at 65°C in TE SDS buffer containing 200 mM NaCl and 0.65 µg/µL proteinase K. DNA was purified using the ChIP DNA clean and concentrator kit (Zymo research). The experiment was done in three biological replicates which were sequenced separately. DNA libraries were prepared using the Illumina TruSeq RNA sample preparation Kit v2 starting from the end repair step of the protocol. Up to 100 ng ChIP DNA was used as starting material. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified for 18 PCR cycles to create the final libraries. After validation (Agilent 2200 TapeStation) and quantification using the KAPA Library Quantification Kit (VWR, Erlangen, Germany) and the Applied Biosystems 7900HT Sequence Detection System, equimolar amounts of library were pooled. The pool was sequenced using the Illumina TruSeq PE Cluster Kit v3 and the Illumina TruSeq SBS Kit v3-HS (101x7x101 Cycles) on an Illumina HiSeq 2000 sequencer with a paired-end (101x7x101 cycles) protocol. Illumina HiSeq 2000 gds 301977395 GEO Accession GSM1977395 SRX1494717 GSM1977396 SRP067656 SRS1217474 GSM1977396 ChIP-Seq GENOMIC ChIP Samples were ground to a fine powder in liquid nitrogen. For chromatin preparation, powder was resuspended in lysis buffer (50mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 5 mM benzamidine, 2 mM PMSF, 1 X Roche complete EDTA free protease inhibitors) and further treated by sonication to lyse the remaining cells using a microtip sonifier (Branson). Chromatin was then sheared in a bioruptor sonication bath (Diagenode) for 10 cycles (30s on / 30s off) at high power setting. An aliquot was saved to serve as input control and the rest of the chromatin solution was incubated with ChIP grade Protein A/G magnetic beads (Life technologies) coupled to a monoclonal anti-HA antibody (Sigma) for 10h at 4°C. Beads were washed three times in lysis buffer, two times in high salt buffer (50 mM HEPES pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 1 X Roche complete EDTA free protease inhibitors) and once in TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 7.5). DNA / Ros1HA complexes were eluted from the beads in TE SDS buffer (10 mM Tris-HCl, 1 mM EDTA, 1% SDS, pH 7.5) by incubation for15 min at 65°C. Samples and input controls were de-crosslinked for 8-10h at 65°C in TE SDS buffer containing 200 mM NaCl and 0.65 µg/µL proteinase K. DNA was purified using the ChIP DNA clean and concentrator kit (Zymo research). The experiment was done in three biological replicates which were sequenced separately. DNA libraries were prepared using the Illumina TruSeq RNA sample preparation Kit v2 starting from the end repair step of the protocol. Up to 100 ng ChIP DNA was used as starting material. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified for 18 PCR cycles to create the final libraries. After validation (Agilent 2200 TapeStation) and quantification using the KAPA Library Quantification Kit (VWR, Erlangen, Germany) and the Applied Biosystems 7900HT Sequence Detection System, equimolar amounts of library were pooled. The pool was sequenced using the Illumina TruSeq PE Cluster Kit v3 and the Illumina TruSeq SBS Kit v3-HS (101x7x101 Cycles) on an Illumina HiSeq 2000 sequencer with a paired-end (101x7x101 cycles) protocol. Illumina HiSeq 2000 gds 301977396 GEO Accession GSM1977396