SRX2900832 GSM2663788 SRP108946 SRS2267674 GSM2663788 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663788 GSM2663788 GEO Accession GSM2663788 SRX2900833 GSM2663789 SRP108946 SRS2267676 GSM2663789 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663789 GSM2663789 GEO Accession GSM2663789 SRX2900834 GSM2663790 SRP108946 SRS2267675 GSM2663790 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663790 GSM2663790 GEO Accession GSM2663790 SRX2900835 GSM2663791 SRP108946 SRS2267677 GSM2663791 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663791 GSM2663791 GEO Accession GSM2663791 SRX2900836 GSM2663792 SRP108946 SRS2267678 GSM2663792 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663792 GSM2663792 GEO Accession GSM2663792 SRX2900837 GSM2663793 SRP108946 SRS2267679 GSM2663793 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663793 GSM2663793 GEO Accession GSM2663793 SRX2900838 GSM2663794 SRP108946 SRS2267680 GSM2663794 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663794 GSM2663794 GEO Accession GSM2663794 SRX2900839 GSM2663795 SRP108946 SRS2267681 GSM2663795 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663795 GSM2663795 GEO Accession GSM2663795 SRX2900840 GSM2663796 SRP108946 SRS2267682 GSM2663796 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663796 GSM2663796 GEO Accession GSM2663796 SRX2900841 GSM2663797 SRP108946 SRS2267683 GSM2663797 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663797 GSM2663797 GEO Accession GSM2663797 SRX2900842 GSM2663798 SRP108946 SRS2267684 GSM2663798 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663798 GSM2663798 GEO Accession GSM2663798 SRX2900843 GSM2663799 SRP108946 SRS2267685 GSM2663799 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663799 GSM2663799 GEO Accession GSM2663799 SRX2900844 GSM2663800 SRP108946 SRS2267686 GSM2663800 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663800 GSM2663800 GEO Accession GSM2663800 SRX2900845 GSM2663801 SRP108946 SRS2267687 GSM2663801 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663801 GSM2663801 GEO Accession GSM2663801 SRX2900846 GSM2663802 SRP108946 SRS2267688 GSM2663802 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663802 GSM2663802 GEO Accession GSM2663802 SRX2900847 GSM2663803 SRP108946 SRS2267689 GSM2663803 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663803 GSM2663803 GEO Accession GSM2663803 SRX2900848 GSM2663804 SRP108946 SRS2267690 GSM2663804 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663804 GSM2663804 GEO Accession GSM2663804 SRX2900849 GSM2663805 SRP108946 SRS2267691 GSM2663805 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663805 GSM2663805 GEO Accession GSM2663805 SRX2900850 GSM2663806 SRP108946 SRS2267692 GSM2663806 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663806 GSM2663806 GEO Accession GSM2663806 SRX2900851 GSM2663807 SRP108946 SRS2267693 GSM2663807 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663807 GSM2663807 GEO Accession GSM2663807 SRX2900852 GSM2663808 SRP108946 SRS2267694 GSM2663808 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663808 GSM2663808 GEO Accession GSM2663808 SRX2900853 GSM2663809 SRP108946 SRS2267695 GSM2663809 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663809 GSM2663809 GEO Accession GSM2663809 SRX2900854 GSM2663810 SRP108946 SRS2267696 GSM2663810 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663810 GSM2663810 GEO Accession GSM2663810 SRX2900855 GSM2663811 SRP108946 SRS2267697 GSM2663811 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663811 GSM2663811 GEO Accession GSM2663811 SRX2900856 GSM2663812 SRP108946 SRS2267698 GSM2663812 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663812 GSM2663812 GEO Accession GSM2663812 SRX2900857 GSM2663813 SRP108946 SRS2267699 GSM2663813 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663813 GSM2663813 GEO Accession GSM2663813 SRX2900858 GSM2663814 SRP108946 SRS2267700 GSM2663814 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663814 GSM2663814 GEO Accession GSM2663814 SRX2900859 GSM2663815 SRP108946 SRS2267701 GSM2663815 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663815 GSM2663815 GEO Accession GSM2663815 SRX2900860 GSM2663816 SRP108946 SRS2267702 GSM2663816 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663816 GSM2663816 GEO Accession GSM2663816 SRX2900861 GSM2663817 SRP108946 SRS2267703 GSM2663817 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663817 GSM2663817 GEO Accession GSM2663817 SRX2900862 GSM2663818 SRP108946 SRS2267704 GSM2663818 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663818 GSM2663818 GEO Accession GSM2663818 SRX2900863 GSM2663819 SRP108946 SRS2267705 GSM2663819 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663819 GSM2663819 GEO Accession GSM2663819 SRX2900864 GSM2663820 SRP108946 SRS2267706 GSM2663820 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663820 GSM2663820 GEO Accession GSM2663820 SRX2900865 GSM2663821 SRP108946 SRS2267707 GSM2663821 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663821 GSM2663821 GEO Accession GSM2663821 SRX2900866 GSM2663822 SRP108946 SRS2267708 GSM2663822 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663822 GSM2663822 GEO Accession GSM2663822 SRX2900867 GSM2663823 SRP108946 SRS2267709 GSM2663823 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663823 GSM2663823 GEO Accession GSM2663823 SRX2900868 GSM2663824 SRP108946 SRS2267710 GSM2663824 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663824 GSM2663824 GEO Accession GSM2663824 SRX2900869 GSM2663825 SRP108946 SRS2267711 GSM2663825 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663825 GSM2663825 GEO Accession GSM2663825 SRX2900870 GSM2663826 SRP108946 SRS2267712 GSM2663826 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663826 GSM2663826 GEO Accession GSM2663826 SRX2900871 GSM2663827 SRP108946 SRS2267713 GSM2663827 MNase-Seq GENOMIC MNase After RNAi treatment, 10^7 S2 or Kc cells were pelleted and washed twice in phosphate-buffered saline (PBS). Next, the cells were crosslinked in 1.1% formaldehyde in PBS for 10 min at room temperature. After quenching the reaction with the addition of 50 μl of 2.5 M glycine, the cells were tumbled at room temperature for 2 min. Cells were next rinsed twice with cold PBS before pelleting and flash freezing in liquid nitrogen. For MNase digestion, cell pellets were resuspended in PBS with 0.1% Triton X-100 (PBS–TX). Approximately 10^6 cells per titration point were digested with either 1.5, 6.25, 25 or 100 U of MNase in a volume of 400 μl PBS–TX supplemented with 1 mM CaCl2 at 37 °C for 3 min. The digestion reaction was stopped by moving tubes to ice and adding 10 μl of 250 mM EDTA, 250 mM EGTA. Next the digestions were adjusted to 0.5%SDS and 10 mM Tris pH 8 before performing DNA cleanup. To clean the DNA, digestions were incubated with RNase (Roche) for 30 min at 37 °C then proteinase K (Roche) for 60 min at 55 °C, followed by incubation at 65 °C for 60 min to reverse crosslinks. A standard phenol-chloroform extraction and ethanol precipitation was next performed. The purified DNA was used as input for library preparation, which is described in detail in Bowman et al (2013). Completed libraries were sequenced on a HiSeq2500 according to manufacturer’s instructions. Preparation of sequencing libraries was performed as described previously in Bowman et al (2013). Illumina HiSeq 2500 gds 302663827 GSM2663827 GEO Accession GSM2663827