SRX4639142 GSM3374805 SRP159554 SRS3737866 GSM3374805 ChIP-Seq GENOMIC ChIP To obtain female embryos, we mated +; SD72/CyO females to 19-3, yw, Rsp[s]-B[s]/Dp(2:y)CB25-4, y+, Rsp[s]B[s]; SPSD/CyO males (both kind gifts from Cynthia Staber) to obtain +/Dp(2:y) CB25-4, y+, Rsp[s]B[s]; SPSD/SD72 males, which we then mated to yw; attP2{ PCNA-EGFP} females (kind gift from Shelby Blythe). We performed 0- to 4-h timed lays and collected and fixed embry- os according to Blythe and Wieschaus (2015). We then hand- sorted embryos using a Zeiss Discovery.V8 microscope under GFP excitation using an X-CITE 120Q stereo light source. We pooled 200 (NC 11–14) to 400 (NC < 11) embryos and performed ChIP as in Blythe and Wieschaus (2015) using 3 μL of rabbit anti-CLAMP antibody per sample. We synthesized libraries using the NEBNext ChIP-seq kit (New England Biosystems) and se- quenced libraries on an Illumina HiSeq 2500 in 2×100-bp mode. We mapped CLAMP ChIP-seq reads to the custom histone locus genome (McKay et al. 2015), allowing only unique alignments by using Bowtie aligner (Langmead et al. 2009). Illumina HiSeq 2500 gds 303374805 GSM3374805 GEO Accession GSM3374805 SRX4639143 GSM3374806 SRP159554 SRS3737867 GSM3374806 ChIP-Seq GENOMIC ChIP To obtain female embryos, we mated +; SD72/CyO females to 19-3, yw, Rsp[s]-B[s]/Dp(2:y)CB25-4, y+, Rsp[s]B[s]; SPSD/CyO males (both kind gifts from Cynthia Staber) to obtain +/Dp(2:y) CB25-4, y+, Rsp[s]B[s]; SPSD/SD72 males, which we then mated to yw; attP2{ PCNA-EGFP} females (kind gift from Shelby Blythe). We performed 0- to 4-h timed lays and collected and fixed embry- os according to Blythe and Wieschaus (2015). We then hand- sorted embryos using a Zeiss Discovery.V8 microscope under GFP excitation using an X-CITE 120Q stereo light source. We pooled 200 (NC 11–14) to 400 (NC < 11) embryos and performed ChIP as in Blythe and Wieschaus (2015) using 3 μL of rabbit anti-CLAMP antibody per sample. We synthesized libraries using the NEBNext ChIP-seq kit (New England Biosystems) and se- quenced libraries on an Illumina HiSeq 2500 in 2×100-bp mode. We mapped CLAMP ChIP-seq reads to the custom histone locus genome (McKay et al. 2015), allowing only unique alignments by using Bowtie aligner (Langmead et al. 2009). Illumina HiSeq 2500 gds 303374806 GSM3374806 GEO Accession GSM3374806 SRX4639144 GSM3374807 SRP159554 SRS3737868 GSM3374807 ChIP-Seq GENOMIC ChIP To obtain female embryos, we mated +; SD72/CyO females to 19-3, yw, Rsp[s]-B[s]/Dp(2:y)CB25-4, y+, Rsp[s]B[s]; SPSD/CyO males (both kind gifts from Cynthia Staber) to obtain +/Dp(2:y) CB25-4, y+, Rsp[s]B[s]; SPSD/SD72 males, which we then mated to yw; attP2{ PCNA-EGFP} females (kind gift from Shelby Blythe). We performed 0- to 4-h timed lays and collected and fixed embry- os according to Blythe and Wieschaus (2015). We then hand- sorted embryos using a Zeiss Discovery.V8 microscope under GFP excitation using an X-CITE 120Q stereo light source. We pooled 200 (NC 11–14) to 400 (NC < 11) embryos and performed ChIP as in Blythe and Wieschaus (2015) using 3 μL of rabbit anti-CLAMP antibody per sample. We synthesized libraries using the NEBNext ChIP-seq kit (New England Biosystems) and se- quenced libraries on an Illumina HiSeq 2500 in 2×100-bp mode. We mapped CLAMP ChIP-seq reads to the custom histone locus genome (McKay et al. 2015), allowing only unique alignments by using Bowtie aligner (Langmead et al. 2009). Illumina HiSeq 2500 gds 303374807 GSM3374807 GEO Accession GSM3374807 SRX4639145 GSM3374808 SRP159554 SRS3737869 GSM3374808 ChIP-Seq GENOMIC ChIP To obtain female embryos, we mated +; SD72/CyO females to 19-3, yw, Rsp[s]-B[s]/Dp(2:y)CB25-4, y+, Rsp[s]B[s]; SPSD/CyO males (both kind gifts from Cynthia Staber) to obtain +/Dp(2:y) CB25-4, y+, Rsp[s]B[s]; SPSD/SD72 males, which we then mated to yw; attP2{ PCNA-EGFP} females (kind gift from Shelby Blythe). We performed 0- to 4-h timed lays and collected and fixed embry- os according to Blythe and Wieschaus (2015). We then hand- sorted embryos using a Zeiss Discovery.V8 microscope under GFP excitation using an X-CITE 120Q stereo light source. We pooled 200 (NC 11–14) to 400 (NC < 11) embryos and performed ChIP as in Blythe and Wieschaus (2015) using 3 μL of rabbit anti-CLAMP antibody per sample. We synthesized libraries using the NEBNext ChIP-seq kit (New England Biosystems) and se- quenced libraries on an Illumina HiSeq 2500 in 2×100-bp mode. We mapped CLAMP ChIP-seq reads to the custom histone locus genome (McKay et al. 2015), allowing only unique alignments by using Bowtie aligner (Langmead et al. 2009). Illumina HiSeq 2500 gds 303374808 GSM3374808 GEO Accession GSM3374808 SRX4639146 GSM3374809 SRP159554 SRS3737870 GSM3374809 ChIP-Seq GENOMIC ChIP To obtain female embryos, we mated +; SD72/CyO females to 19-3, yw, Rsp[s]-B[s]/Dp(2:y)CB25-4, y+, Rsp[s]B[s]; SPSD/CyO males (both kind gifts from Cynthia Staber) to obtain +/Dp(2:y) CB25-4, y+, Rsp[s]B[s]; SPSD/SD72 males, which we then mated to yw; attP2{ PCNA-EGFP} females (kind gift from Shelby Blythe). We performed 0- to 4-h timed lays and collected and fixed embry- os according to Blythe and Wieschaus (2015). We then hand- sorted embryos using a Zeiss Discovery.V8 microscope under GFP excitation using an X-CITE 120Q stereo light source. We pooled 200 (NC 11–14) to 400 (NC < 11) embryos and performed ChIP as in Blythe and Wieschaus (2015) using 3 μL of rabbit anti-CLAMP antibody per sample. We synthesized libraries using the NEBNext ChIP-seq kit (New England Biosystems) and se- quenced libraries on an Illumina HiSeq 2500 in 2×100-bp mode. We mapped CLAMP ChIP-seq reads to the custom histone locus genome (McKay et al. 2015), allowing only unique alignments by using Bowtie aligner (Langmead et al. 2009). Illumina HiSeq 2500 gds 303374809 GSM3374809 GEO Accession GSM3374809 SRX4639147 GSM3374810 SRP159554 SRS3737871 GSM3374810 ChIP-Seq GENOMIC ChIP To obtain female embryos, we mated +; SD72/CyO females to 19-3, yw, Rsp[s]-B[s]/Dp(2:y)CB25-4, y+, Rsp[s]B[s]; SPSD/CyO males (both kind gifts from Cynthia Staber) to obtain +/Dp(2:y) CB25-4, y+, Rsp[s]B[s]; SPSD/SD72 males, which we then mated to yw; attP2{ PCNA-EGFP} females (kind gift from Shelby Blythe). We performed 0- to 4-h timed lays and collected and fixed embry- os according to Blythe and Wieschaus (2015). We then hand- sorted embryos using a Zeiss Discovery.V8 microscope under GFP excitation using an X-CITE 120Q stereo light source. We pooled 200 (NC 11–14) to 400 (NC < 11) embryos and performed ChIP as in Blythe and Wieschaus (2015) using 3 μL of rabbit anti-CLAMP antibody per sample. We synthesized libraries using the NEBNext ChIP-seq kit (New England Biosystems) and se- quenced libraries on an Illumina HiSeq 2500 in 2×100-bp mode. We mapped CLAMP ChIP-seq reads to the custom histone locus genome (McKay et al. 2015), allowing only unique alignments by using Bowtie aligner (Langmead et al. 2009). Illumina HiSeq 2500 gds 303374810 GSM3374810 GEO Accession GSM3374810 SRX4639148 GSM3374811 SRP159554 SRS3737872 GSM3374811 ChIP-Seq GENOMIC ChIP To obtain female embryos, we mated +; SD72/CyO females to 19-3, yw, Rsp[s]-B[s]/Dp(2:y)CB25-4, y+, Rsp[s]B[s]; SPSD/CyO males (both kind gifts from Cynthia Staber) to obtain +/Dp(2:y) CB25-4, y+, Rsp[s]B[s]; SPSD/SD72 males, which we then mated to yw; attP2{ PCNA-EGFP} females (kind gift from Shelby Blythe). We performed 0- to 4-h timed lays and collected and fixed embry- os according to Blythe and Wieschaus (2015). We then hand- sorted embryos using a Zeiss Discovery.V8 microscope under GFP excitation using an X-CITE 120Q stereo light source. We pooled 200 (NC 11–14) to 400 (NC < 11) embryos and performed ChIP as in Blythe and Wieschaus (2015) using 3 μL of rabbit anti-CLAMP antibody per sample. We synthesized libraries using the NEBNext ChIP-seq kit (New England Biosystems) and se- quenced libraries on an Illumina HiSeq 2500 in 2×100-bp mode. We mapped CLAMP ChIP-seq reads to the custom histone locus genome (McKay et al. 2015), allowing only unique alignments by using Bowtie aligner (Langmead et al. 2009). Illumina HiSeq 2500 gds 303374811 GSM3374811 GEO Accession GSM3374811 SRX4639149 GSM3374812 SRP159554 SRS3737873 GSM3374812 ChIP-Seq GENOMIC ChIP To obtain female embryos, we mated +; SD72/CyO females to 19-3, yw, Rsp[s]-B[s]/Dp(2:y)CB25-4, y+, Rsp[s]B[s]; SPSD/CyO males (both kind gifts from Cynthia Staber) to obtain +/Dp(2:y) CB25-4, y+, Rsp[s]B[s]; SPSD/SD72 males, which we then mated to yw; attP2{ PCNA-EGFP} females (kind gift from Shelby Blythe). We performed 0- to 4-h timed lays and collected and fixed embry- os according to Blythe and Wieschaus (2015). We then hand- sorted embryos using a Zeiss Discovery.V8 microscope under GFP excitation using an X-CITE 120Q stereo light source. We pooled 200 (NC 11–14) to 400 (NC < 11) embryos and performed ChIP as in Blythe and Wieschaus (2015) using 3 μL of rabbit anti-CLAMP antibody per sample. We synthesized libraries using the NEBNext ChIP-seq kit (New England Biosystems) and se- quenced libraries on an Illumina HiSeq 2500 in 2×100-bp mode. We mapped CLAMP ChIP-seq reads to the custom histone locus genome (McKay et al. 2015), allowing only unique alignments by using Bowtie aligner (Langmead et al. 2009). Illumina HiSeq 2500 gds 303374812 GSM3374812 GEO Accession GSM3374812