GSM1689672 embryo_2-4 GSM1689679 GSE68983, gd7 embryos 2-4 hr after egg deposition, H3K27ac ChIP-Seq UCSC dm3, 2-4 hr after egg deposition gd7_h3k27ac_2 bw_0_1_2_4_dm3 GSM1689672_gd7_h3k27ac_2.bw GSM1689671 embryo_2-4 GSM1689679 GSE68983, gd7 embryos 2-4 hr after egg deposition, H3K27ac ChIP-Seq UCSC dm3, 2-4 hr after egg deposition gd7_h3k27ac_1 bw_0_1_2_4_dm3 GSM1689671_gd7_h3k27ac_1.bw GSM1689677 embryo_2-4 GSM1689679 GSE68983, gd7 embryos 2-4 hr after egg deposition, mad ChIP-Seq UCSC dm3, 2-4 hr after egg deposition gd7_mad_1 bw_0_1_2_4_dm3 GSM1689677_gd7_mad_1.bw GSM1689675 embryo_2-4 GSM1689679 GSE68983, gd7 embryos 2-4 hr after egg deposition, H3K4me1 ChIP-Seq UCSC dm3, 2-4 hr after egg deposition gd7_h3k4me1_1 bw_0_1_2_4_dm3 GSM1689675_gd7_h3k4me1_1.bw GSM1689676 embryo_2-4 GSM1689680 GSE68983, gd7 embryos 2-4 hr after egg deposition, H3K4me1 ChIP-Seq UCSC dm3, 2-4 hr after egg deposition gd7_h3k4me1_2 bw_0_1_2_4_dm3 GSM1689676_gd7_h3k4me1_2.bw GSM1689678 embryo_2-4 GSM1689680 GSE68983, gd7 embryos 2-4 hr after egg deposition, Custom GenScript Mad ChIP-Seq UCSC dm3, 2-4 hr after egg deposition gd7_mad_2 bw_0_1_2_4_dm3 GSM1689678_gd7_mad_2.bw GSM1689682 embryo_2-4 GSM1689679 GSE68983, gd7 embryos 2-4 hr after egg deposition, Custom GenScript Zen ChIP-Seq UCSC dm3, 2-4 hr after egg deposition gd7_zen_1 bw_0_1_2_4_dm3 GSM1689682_gd7_zen_1.bw GSM1689687 embryo_2-4 GSM1689689 GSE68983, orer embryos 2-4 hr after egg deposition, Pc ChIP-Seq UCSC dm3, 2-4 hr after egg deposition orer_pc_1 bw_0_1_2_4_dm3 GSM1689687_orer_pc_1.bw GSM1689688 embryo_2-4 GSM1689689 GSE68983, orer embryos 2-4 hr after egg deposition, Custom GenScript Sna 134626-2 ChIP-Seq UCSC dm3, 2-4 hr after egg deposition orer_sna_1 bw_0_1_2_4_dm3 GSM1689688_orer_sna_1.bw GSM1689683 embryo_2-4 GSM1689680 GSE68983, gd7 embryos 2-4 hr after egg deposition, Custom GenScript Zen ChIP-Seq UCSC dm3, 2-4 hr after egg deposition gd7_zen_2 bw_0_1_2_4_dm3 GSM1689683_gd7_zen_2.bw GSM1689686 embryo_2-4 GSM1689689 GSE68983, orer embryos 2-4 hr after egg deposition, Custom GenScript Trl 163185-42 ChIP-Seq UCSC dm3, 2-4 hr after egg deposition orer_gaf_1 bw_0_1_2_4_dm3 GSM1689686_orer_gaf_1.bw GSM1689691 embryo_2-4 GSM1689700 GSE68983, tl10b embryos 2-4 hr after egg deposition, Custom GenScript Dl 126740-44 ChIP-Seq UCSC dm3, 2-4 hr after egg deposition tl10b_dl_2 bw_0_1_2_4_dm3 GSM1689691_tl10b_dl_2.bw GSM1689693 embryo_2-4 GSM1689700 GSE68983, tl10b embryos 2-4 hr after egg deposition, H3K27ac ChIP-Seq UCSC dm3, 2-4 hr after egg deposition tl10b_h3k27ac_3 bw_0_1_2_4_dm3 GSM1689693_tl10b_h3k27ac_3.bw GSM1689692 embryo_2-4 GSM1689700 GSE68983, tl10b embryos 2-4 hr after egg deposition, H3K27ac ChIP-Seq UCSC dm3, 2-4 hr after egg deposition tl10b_h3k27ac_1 bw_0_1_2_4_dm3 GSM1689692_tl10b_h3k27ac_1.bw GSM1689690 embryo_2-4 GSM1689700 GSE68983, tl10b embryos 2-4 hr after egg deposition, Custom GenScript Dl 126740-44 ChIP-Seq UCSC dm3, 2-4 hr after egg deposition tl10b_dl_1 bw_0_1_2_4_dm3 GSM1689690_tl10b_dl_1.bw GSM1689696 embryo_2-4 GSM1689700 GSE68983, tl10b embryos 2-4 hr after egg deposition, H3K4me1 ChIP-Seq UCSC dm3, 2-4 hr after egg deposition tl10b_h3k4me1_1 bw_0_1_2_4_dm3 GSM1689696_tl10b_h3k4me1_1.bw GSM1689697 embryo_2-4 GSM1689700 GSE68983, tl10b embryos 2-4 hr after egg deposition, H3K4me1 ChIP-Seq UCSC dm3, 2-4 hr after egg deposition tl10b_h3k4me1_3 bw_0_1_2_4_dm3 GSM1689697_tl10b_h3k4me1_3.bw GSM1689698 embryo_2-4 GSM1689700 GSE68983, tl10b embryos 2-4 hr after egg deposition, Custom Covance Twi ChIP-Seq UCSC dm3, 2-4 hr after egg deposition tl10b_twi_1 bw_0_1_2_4_dm3 GSM1689698_tl10b_twi_1.bw GSM1689699 embryo_2-4 GSM1689700 GSE68983, tl10b embryos 2-4 hr after egg deposition, Custom Covance Twi ChIP-Seq UCSC dm3, 2-4 hr after egg deposition tl10b_twi_2 bw_0_1_2_4_dm3 GSM1689699_tl10b_twi_2.bw GSM2285339 embryo_2-4 GSE68983, Oregon-R embryos 2-4 hr after egg deposition, ATAC-Seq UCSC dm3, UCSC dm3, 2-4 hr after egg deposition orer_atac_1 bw_0_1_2_4_dm3 GSM2285339_orer_atac_1.bw GSM2285344 embryo_2-4 GSM1689679 GSE68983, gd7 embryos 2-4 hr after egg deposition, gd7_zld_1,ChIP-seq for Zelda in gd7 ChIP-Seq UCSC dm3, UCSC dm3, 2-4 hr after egg deposition gd7_zld_1 bw_0_1_2_4_dm3 GSM2285344_gd7_zld_1.bw GSM2285343 embryo_2-4 GSM1689700 GSE68983, tl10b embryos 2-4 hr after egg deposition, tl10b_zld_2,ChIP-seq for Zelda in Toll10b ChIP-Seq UCSC dm3, UCSC dm3, 2-4 hr after egg deposition tl10b_zld_2 bw_0_1_2_4_dm3 GSM2285343_tl10b_zld_2.bw GSM2285342 embryo_2-4 GSM1689700 GSE68983, tl10b embryos 2-4 hr after egg deposition, tl10b_zld_1,ChIP-seq for Zelda in Toll10b ChIP-Seq UCSC dm3, UCSC dm3, 2-4 hr after egg deposition tl10b_zld_1 bw_0_1_2_4_dm3 GSM2285342_tl10b_zld_1.bw GSM2285341 embryo_2-4 GSM1689689 GSE68983, Oregon-R embryos 2-4 hr after egg deposition, orer_nej_1,ChIP-seq for Nejire in OregonR ChIP-Seq UCSC dm3, UCSC dm3, 2-4 hr after egg deposition orer_nej_1 bw_0_1_2_4_dm3 GSM2285341_orer_nej_1.bw GSM2285340 embryo_2-4 GSE68983, Oregon-R embryos 2-4 hr after egg deposition, ATAC-Seq UCSC dm3, UCSC dm3, 2-4 hr after egg deposition orer_atac_2 bw_0_1_2_4_dm3 GSM2285340_orer_atac_2.bw GSM2285346 embryo_2-4 GSM1689700 GSE68983, tl10b embryos 2-4 hr after egg deposition, H3K27ac ChIP-Seq UCSC dm3, UCSC dm3, 2-4 hr after egg deposition tl10b_h3k27ac_4 bw_0_1_2_4_dm3 GSM2285346_tl10b_h3k27ac_4.bw GSM2285345 embryo_2-4 GSM1689680 GSE68983, gd7 embryos 2-4 hr after egg deposition, gd7_zld_2,ChIP-seq for Zelda in gd7 ChIP-Seq UCSC dm3, UCSC dm3, 2-4 hr after egg deposition gd7_zld_2 bw_0_1_2_4_dm3 GSM2285345_gd7_zld_2.bw GSM1596243 embryo_2-4 GSE65441, embryos input MNase-Seq dm3, developmental stage (after egg laying): 2-4h 2-4h wt MNase-seq rep1 bw_0_1_2_4_dm3 GSM1596243_2-4h_wt_MNase-seq_rep1.bw GSM1596245 embryo_2-4 GSE65441, embryos input MNase-Seq dm3, developmental stage (after egg laying): 2-4h 2-4h wt MNase-seq rep2 bw_0_1_2_4_dm3 GSM1596245_2-4h_wt_MNase-seq_rep2.bw GSM1341814 embryo_2-4 GSE55306, whole-embryo, Dorsal ChIP-seq Rep 1 Oregon-R, Dorsal , custom ChIP-Seq dm3, whole-embryo Dorsal ChIP-seq (Drosophila embryos) Rep 1 bw_0_1_2_4_dm3 GSM1341814_dmel_embryo_dl_chipseq_01.bw GSM1430016 embryo_2-4 GSE55306, whole-embryo, Oregon-R_embryo Oregon-R, Twist , custom ChIP-Seq UCSC dm3, whole-embryo Twist ChIP-seq (Drosophila embryos) Rep 1 bw_0_1_2_4_dm3 GSM1430016_dmel_embryo_twi_chipseq_01.bw GSM1444488 embryo_2-4 GSM1444489 GSE59726, embryo, Whole cell embryonic extract 2-4 hour embryo, yw, Santa cruz #sc-25761 ChIP-Seq dm3, 2-4 hour embryo Su(H) 2-4 hr rabbit-ab IP rep2 bd_0_1_2_6_dm3 UsingSRR GSM1444487 embryo_2-4 GSM1444489 GSE59726, embryo, Whole cell embryonic extract 2-4 hour embryo, yw, Santa cruz #sc-25761 ChIP-Seq dm3, 2-4 hour embryo Su(H) 2-4 hr rabbit-ab IP rep1 bd_0_1_2_6_dm3 UsingSRR GSM1444485 embryo_2-4 GSM1444489 GSE59726, embryo, Whole cell embryonic extract 2-4 hour embryo, yw, Santa cruz goat #sc-15813 ChIP-Seq dm3, 2-4 hour embryo Su(H) 2-4 hr goat-ab IP rep1 bd_0_1_2_6_dm3 UsingSRR GSM1444486 embryo_2-4 GSM1444489 GSE59726, embryo, Whole cell embryonic extract 2-4 hour embryo, yw, Santa cruz goat #sc-15813 ChIP-Seq dm3, 2-4 hour embryo Su(H) 2-4 hr goat-ab IP rep2 bd_0_1_2_6_dm3 UsingSRR GSM1257808 embryo_2-4 GSE52029, Staged embryos 2-4h AEL, TBP 517 ChIP-Seq Release 5, genotype: Oregon-R TBP 517 Antibody bg_0_1_2_4_dm3 GSM1257808_tbp_2to4h_517_1.bedgraph.gz GSM1257809 embryo_2-4 GSE52029, Staged embryos 2-4h AEL, TBP 518 ChIP-Seq Release 5, genotype: Oregon-R TBP 518 Antibody bg_0_1_2_4_dm3 GSM1257809_tbp_2to4h_518_1.bedgraph.gz GSM1257811 embryo_2-4 GSE52029, Staged embryos 2-4h AEL, Trf2 275 ChIP-Seq Release 5, genotype: Oregon-R Trf2 275 Antibody bg_0_1_2_4_dm3 GSM1257811_trf2_2to4h_275_1.bedgraph.gz GSM1257810 embryo_2-4 GSE52029, Staged embryos 2-4h AEL, Trf2 274 ChIP-Seq Release 5, genotype: Oregon-R Trf2 274 Antibody bg_0_1_2_4_dm3 GSM1257810_trf2_2to4h_274_1.bedgraph.gz GSM998949 embryo_2-4 GSM998954 GSE40664, whole-embryo, Twist ChIP-Seq from 2-4 h wild type embryos Oregon R (wild type), Twist ChIP-Seq UCSC dm3, Oregon R (wild type) Twist ChIP-Seq from 2-4 h wild type embryos, rep2 bd_0_1_2_6_dm3 UsingSRR GSM998948 embryo_2-4 GSM998953 GSE40664, whole-embryo, Twist ChIP-Seq from 2-4 h wild type embryos Oregon R (wild type), Twist ChIP-Seq UCSC dm3, Oregon R (wild type) Twist ChIP-Seq from 2-4 h wild type embryos, rep1 bd_0_1_2_6_dm3 UsingSRR GSM998951 embryo_2-4 GSM998956 GSE40664, whole-embryo, Twist ChIP-Seq from 2-4 h wild type embryos Oregon R (wild type), Twist ChIP-Seq UCSC dm3, Oregon R (wild type) Twist ChIP-Seq from 2-4 h wild type embryos, rep4 bd_0_1_2_6_dm3 UsingSRR GSM998950 embryo_2-4 GSM998955 GSE40664, whole-embryo, Twist ChIP-Seq from 2-4 h wild type embryos Oregon R (wild type), Twist ChIP-Seq UCSC dm3, Oregon R (wild type) Twist ChIP-Seq from 2-4 h wild type embryos, rep3 bd_0_1_2_6_dm3 UsingSRR GSM998952 embryo_2-4 GSM998957 GSE40664, whole-embryo, Twist ChIP-Seq from 2-4 h wild type embryos Oregon R (wild type), Twist ChIP-Seq UCSC dm3, Oregon R (wild type) Twist ChIP-Seq from 2-4 h wild type embryos, rep5 bd_0_1_2_6_dm3 UsingSRR GSM948712 embryo_2-4 GSE38727, whole embryo, 2-4 hour embryos 2-4 hours after egg laying, OregonR, FAIRE dm3, OregonR e2-4hr_faire bd_0_1_2_4_dm3 GSM948712_e2-4hr_FAIRE_peaks.bed.gz GSM1022624 embryo_2-4 GSE41686,GSE41703, Staged embryos MBT 02to03h AEL, MNase UCSC dm3, MBT 02to03h AEL Mnase-seq in MBT staged embryos bd_0_1_2_6_dm3 UsingSRR GSM1022897 embryo_2-4 GSM1022900 GSE41700,GSE41703, Staged embryos MBT 02to03h AEL, POLR2A ChIP-Seq UCSC dm3, MBT 02to03h AEL ChIP-seq Pol II in MBT embryos (replicate 3) bd_0_1_2_6_dm3 UsingSRR GSM1022899 embryo_2-4 GSM1022900 GSE41700,GSE41703, Staged embryos MBT 02to03h AEL, TBP ChIP-Seq UCSC dm3, MBT 02to03h AEL ChIP-seq TBP in MBT embryos (replicate 2) bd_0_1_2_6_dm3 UsingSRR GSM1022896 embryo_2-4 GSM1022900 GSE41700,GSE41703, Staged embryos MBT 02to03h AEL, POLR2A ChIP-Seq UCSC dm3, MBT 02to03h AEL ChIP-seq Pol II in MBT embryos (replicate 2) bd_0_1_2_6_dm3 UsingSRR GSM1022898 embryo_2-4 GSM1022900 GSE41700,GSE41703, Staged embryos MBT 02to03h AEL, TBP ChIP-Seq UCSC dm3, MBT 02to03h AEL ChIP-seq TBP in MBT embryos (replicate 1) bd_0_1_2_6_dm3 UsingSRR GSM1022895 embryo_2-4 GSM1022900 GSE41700,GSE41703, Staged embryos MBT 02to03h AEL, POLR2A ChIP-Seq UCSC dm3, MBT 02to03h AEL ChIP-seq Pol II in MBT embryos (replicate 1) bd_0_1_2_6_dm3 UsingSRR GSM1022903 embryo_2-4 GSM1022904 GSE41700,GSE41703, Staged embryos post-MBT 02to04h AEL, TBP ChIP-Seq UCSC dm3, post-MBT 02to04h AEL ChIP-seq TBP in post-MBT embryos (replicate 1) bd_0_1_2_6_dm3 UsingSRR GSM1022902 embryo_2-4 GSM1022904 GSE41700,GSE41703, Staged embryos post-MBT 02to04h AEL, POLR2A ChIP-Seq UCSC dm3, post-MBT 02to04h AEL ChIP-seq Pol II in post-MBT embryos (replicate 1) bd_0_1_2_6_dm3 UsingSRR GSM846338 embryo_2-4 GSE34283,GSE34304, Toll10b mutant MNase genetic background: embryos were collected from Toll10b/+ females obtained from a balanced stock (Toll10b/TM3, Sb, Ser and Toll10b/OR60) Toll10b mutant MNase-seq bd_0_1_2_6_dm3 UsingSRR GSM846920 embryo_2-4 GSE34301,GSE34304, Oregon R POLR2A ChIP-Seq genetic background: Oregon R Pol II ChIP-seq from 2-4 h wild type embryos, 4H8 antibody, replicate 1 bd_0_1_2_6_dm3 UsingSRR GSM844812 embryo_2-4 GSM844814 GSE34221, WT_CBP ChIP 2-4h embryo, rabbit Drosophila CBP ChIP-Seq genotype/variation: w1118 (wild type) CBP w bd_0_1_2_6_dm3 UsingSRR