GSM3477028 Embryo_mixed NA GSE122639 whole worms mixed embryo N2 MDT-15 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. MDT-15 N2 emb rep2 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3477027 Embryo_mixed NA GSE122639 whole worms mixed embryo N2 MDT-15 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. MDT-15 N2 emb rep1 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3477023 Embryo_mixed NA GSE122639 whole worms mixed embryo N2 CBP-1 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. CBP-1 N2 emb rep2 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3477022 Embryo_mixed NA GSE122639 whole worms mixed embryo N2 CBP-1 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. CBP-1 N2 emb rep1 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3477019 Embryo_mixed NA GSE122639 whole worms mixed embryo CB428 POLR2A ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. RNA Pol II CB428 emb rep2 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3477018 Embryo_mixed NA GSE122639 whole worms mixed embryo CB428 POLR2A ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. RNA Pol II CB428 emb rep1 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3477017 Embryo_mixed NA GSE122639 whole worms mixed embryo N2 POLR2A ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. RNA Pol II N2 emb rep2 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3477016 Embryo_mixed NA GSE122639 whole worms mixed embryo N2 POLR2A ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. RNA Pol II N2 emb rep1 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3477015 Embryo_mixed NA GSE122639 whole worms mixed embryo N2 AMA-1 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. AMA1 N2 DPY-27 RNAi emb rep2 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3477014 Embryo_mixed NA GSE122639 whole worms mixed embryo N2 AMA-1 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. AMA1 N2 DPY-27 RNAi emb rep1 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3476972 Embryo_mixed NA GSE122639 whole worms mixed embryo N2 H3K27ac ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. H3K27ac N2 DPY-27 RNAi emb rep2 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3476971 Embryo_mixed NA GSE122639 whole worms mixed embryo N2 H3K27ac ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. H3K27ac N2 DPY-27 RNAi emb rep1 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3476970 Embryo_mixed NA GSE122639 whole worms mixed embryo CB428 H3K27ac ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. H3K27ac CB428 emb rep2 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3476969 Embryo_mixed NA GSE122639 whole worms mixed embryo CB428 H3K27ac ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. H3K27ac CB428 emb rep1 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3476968 Embryo_mixed NA GSE122639 whole worms mixed embryo N2 H3K27ac ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. H3K27ac N2 emb rep3 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3476967 Embryo_mixed NA GSE122639 whole worms mixed embryo N2 H3K27ac ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. H3K27ac N2 emb rep2 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3476966 Embryo_mixed NA GSE122639 whole worms mixed embryo N2 H3K27ac ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. H3K27ac N2 emb rep1 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3476963 Embryo_mixed NA GSE122639 whole worms mixed embryo CB428 H3K4me1 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. H3K4me1 CB428 emb rep2 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3476962 Embryo_mixed NA GSE122639 whole worms mixed embryo CB428 H3K4me1 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. H3K4me1 CB428 emb rep1 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3476960 Embryo_mixed NA GSE122639 whole worms mixed embryo N2 H3K4me1 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. H3K4me1 N2 DPY-27 RNAi emb rep1 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3476961 Embryo_mixed NA GSE122639 whole worms mixed embryo N2 H3K4me1 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. H3K4me1 N2 DPY-27 RNAi emb rep2 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3476959 Embryo_mixed NA GSE122639 whole worms mixed embryo N2 H3K4me1 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. H3K4me1 N2 Control RNAi emb rep2 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3476958 Embryo_mixed NA GSE122639 whole worms mixed embryo N2 H3K4me1 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. H3K4me1 N2 Control RNAi emb rep1 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3476956 Embryo_mixed NA GSE122639 whole worms mixed embryo N2 H3K4me1 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. H3K4me1 N2 emb rep1 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3477024 Embryo_mixed NA GSE122639 whole worms mixed embryo N2 CBP-1 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. CBP-1 N2 emb rep3 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3477021 Embryo_mixed NA GSE122639 whole worms mixed embryo GW638 POLR2A ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. RNA Pol II GW638 emb rep2 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3477020 Embryo_mixed NA GSE122639 whole worms mixed embryo GW638 POLR2A ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. RNA Pol II GW638 emb rep1 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3477013 Embryo_mixed NA GSE122639 whole worms mixed embryo GW638 CAPG-1 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. CAPG1 GW638 emb rep2 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3477012 Embryo_mixed NA GSE122639 whole worms mixed embryo GW638 CAPG-1 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. CAPG1 GW638 emb rep1 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3477011 Embryo_mixed NA GSE122639 whole worms mixed embryo GW638 SDC-3 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. SDC3 GW638 emb rep2 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3477010 Embryo_mixed NA GSE122639 whole worms mixed embryo GW638 SDC-3 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. SDC3 GW638 emb rep1 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3476957 Embryo_mixed NA GSE122639 whole worms mixed embryo N2 H3K4me1 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. H3K4me1 N2 emb rep2 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM3141755 Embryo_mixed NA GSE114494 mixed embryos N2 H3K4me1 ChIP-Seq cel2 ChIP-seq reads were aligned to the WS220 assembly of the C. elegans genome using bwa. H3K4me1_wt_emb_rep2 bd_0_1_2_6_ce10 UsingSRR GSM3141754 Embryo_mixed NA GSE114494 mixed embryos N2 H3K4me1 ChIP-Seq cel2 ChIP-seq reads were aligned to the WS220 assembly of the C. elegans genome using bwa. H3K4me1_wt_emb_rep1 bd_0_1_2_6_ce10 UsingSRR GSM3141721 Embryo_mixed NA GSE114494 mixed embryos wild-type N2 ATAC-Seq cel2 Reads were trimmed using trim_galore, and aligned using bwa in single-end mode. wt_emb_ATAC-seq_rep2 bd_0_1_2_6_ce10 UsingSRR GSM3141720 Embryo_mixed NA GSE114494 mixed embryos wild-type N2 ATAC-Seq cel2 Reads were trimmed using trim_galore, and aligned using bwa in single-end mode. wt_emb_ATAC-seq_rep1 bd_0_1_2_6_ce10 UsingSRR GSM3142756 Embryo_mixed NA GSE114494 mixed embryos wild-type N2 MNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_emb_MNase-seq_rep2_0.5U_ml bw_0_1_2_4_ce10 GSM3142756_mnase_wt_emb_rep2_0.5U_ml.bw GSM3142755 Embryo_mixed NA GSE114494 mixed embryos wild-type N2 MNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_emb_MNase-seq_rep2_0.25U_ml bw_0_1_2_4_ce10 GSM3142755_mnase_wt_emb_rep2_0.25U_ml.bw GSM3142754 Embryo_mixed NA GSE114494 mixed embryos wild-type N2 MNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_emb_MNase-seq_rep2_0.1U_ml bw_0_1_2_4_ce10 GSM3142754_mnase_wt_emb_rep2_0.1U_ml.bw GSM3142753 Embryo_mixed NA GSE114494 mixed embryos wild-type N2 MNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_emb_MNase-seq_rep2_0.05U_ml bw_0_1_2_4_ce10 GSM3142753_mnase_wt_emb_rep2_0.05U_ml.bw GSM3142752 Embryo_mixed NA GSE114494 mixed embryos wild-type N2 MNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_emb_MNase-seq_rep2_0.025U_ml bw_0_1_2_4_ce10 GSM3142752_mnase_wt_emb_rep2_0.025U_ml.bw GSM3142747 Embryo_mixed NA GSE114494 mixed embryos wild-type N2 MNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_emb_MNase-seq_rep1_0.5U_ml bw_0_1_2_4_ce10 GSM3142747_mnase_wt_emb_rep1_0.5U_ml.bw GSM3142746 Embryo_mixed NA GSE114494 mixed embryos wild-type N2 MNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_emb_MNase-seq_rep1_0.25U_ml bw_0_1_2_4_ce10 GSM3142746_mnase_wt_emb_rep1_0.25U_ml.bw GSM3142745 Embryo_mixed NA GSE114494 mixed embryos wild-type N2 MNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_emb_MNase-seq_rep1_0.1U_ml bw_0_1_2_4_ce10 GSM3142745_mnase_wt_emb_rep1_0.1U_ml.bw GSM3142656 Embryo_mixed NA GSE114494 mixed embryos wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_emb_DNase-seq_rep2_800U_ml bw_0_1_2_4_ce10 GSM3142656_dnase_wt_emb_rep2_800U_ml.bw GSM3142655 Embryo_mixed NA GSE114494 mixed embryos wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_emb_DNase-seq_rep2_400U_ml bw_0_1_2_4_ce10 GSM3142655_dnase_wt_emb_rep2_400U_ml.bw GSM3142654 Embryo_mixed NA GSE114494 mixed embryos wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_emb_DNase-seq_rep2_200U_ml bw_0_1_2_4_ce10 GSM3142654_dnase_wt_emb_rep2_200U_ml.bw GSM3142653 Embryo_mixed NA GSE114494 mixed embryos wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_emb_DNase-seq_rep2_100U_ml bw_0_1_2_4_ce10 GSM3142653_dnase_wt_emb_rep2_100U_ml.bw GSM3142652 Embryo_mixed NA GSE114494 mixed embryos wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_emb_DNase-seq_rep2_50U_ml bw_0_1_2_4_ce10 GSM3142652_dnase_wt_emb_rep2_50U_ml.bw GSM3142651 Embryo_mixed NA GSE114494 mixed embryos wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_emb_DNase-seq_rep2_25U_ml bw_0_1_2_4_ce10 GSM3142651_dnase_wt_emb_rep2_25U_ml.bw GSM3142650 Embryo_mixed NA GSE114494 mixed embryos wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_emb_DNase-seq_rep2_10U_ml bw_0_1_2_4_ce10 GSM3142650_dnase_wt_emb_rep2_10U_ml.bw GSM3142649 Embryo_mixed NA GSE114494 mixed embryos wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_emb_DNase-seq_rep2_5U_ml bw_0_1_2_4_ce10 GSM3142649_dnase_wt_emb_rep2_5U_ml.bw GSM3142648 Embryo_mixed NA GSE114494 mixed embryos wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_emb_DNase-seq_rep2_2.5U_ml bw_0_1_2_4_ce10 GSM3142648_dnase_wt_emb_rep2_2.5U_ml.bw GSM3142647 Embryo_mixed NA GSE114494 mixed embryos wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_emb_DNase-seq_rep1_800U_ml bw_0_1_2_4_ce10 GSM3142647_dnase_wt_emb_rep1_800U_ml.bw GSM3142646 Embryo_mixed NA GSE114494 mixed embryos wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_emb_DNase-seq_rep1_400U_ml bw_0_1_2_4_ce10 GSM3142646_dnase_wt_emb_rep1_400U_ml.bw GSM3142645 Embryo_mixed NA GSE114494 mixed embryos wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_emb_DNase-seq_rep1_200U_ml bw_0_1_2_4_ce10 GSM3142645_dnase_wt_emb_rep1_200U_ml.bw GSM3142644 Embryo_mixed NA GSE114494 mixed embryos wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_emb_DNase-seq_rep1_100U_ml bw_0_1_2_4_ce10 GSM3142644_dnase_wt_emb_rep1_100U_ml.bw GSM3142643 Embryo_mixed NA GSE114494 mixed embryos wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_emb_DNase-seq_rep1_50U_ml bw_0_1_2_4_ce10 GSM3142643_dnase_wt_emb_rep1_50U_ml.bw GSM3142642 Embryo_mixed NA GSE114494 mixed embryos wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_emb_DNase-seq_rep1_25U_ml bw_0_1_2_4_ce10 GSM3142642_dnase_wt_emb_rep1_25U_ml.bw GSM3142641 Embryo_mixed NA GSE114494 mixed embryos wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_emb_DNase-seq_rep1_10U_ml bw_0_1_2_4_ce10 GSM3142641_dnase_wt_emb_rep1_10U_ml.bw GSM3142640 Embryo_mixed NA GSE114494 mixed embryos wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_emb_DNase-seq_rep1_5U_ml bw_0_1_2_4_ce10 GSM3142640_dnase_wt_emb_rep1_5U_ml.bw GSM3142639 Embryo_mixed NA GSE114494 mixed embryos wild-type N2 DNase cel2 Reads were trimmed using trim_galore, and aligned using bwa in paired-end mode. wt_emb_DNase-seq_rep1_2.5U_ml bw_0_1_2_4_ce10 GSM3142639_dnase_wt_emb_rep1_2.5U_ml.bw GSM2339620 Embryo_mixed NA GSE87741 whole worms mixed embryo TY2205 SDC-2 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. SDC2 TY2205 MxEmb rep1 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339609 Embryo_mixed NA GSE87741 whole worms mixed embryo N2 DPY-27 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY27 N2 MxEmb rep1 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339606 Embryo_mixed NA GSE87741 whole worms mixed embryo N2 DPY-30 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY30 N2 MxEmb rep3 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339605 Embryo_mixed NA GSE87741 whole worms mixed embryo N2 DPY-30 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY30 N2 MxEmb rep2 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339604 Embryo_mixed NA GSE87741 whole worms mixed embryo N2 DPY-30 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY30 N2 MxEmb rep1 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339599 Embryo_mixed NA GSE87741 whole worms mixed embryo N2 SDC-3 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. SDC3 N2 MxEmb rep1 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339595 Embryo_mixed NA GSE87741 whole worms mixed embryo N2 SDC-2 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. SDC2 N2 MxEmb rep2 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339594 Embryo_mixed NA GSE87741 whole worms mixed embryo N2 SDC-2 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. SDC2 N2 MxEmb rep1 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339669 Embryo_mixed NA GSE87741 whole worms mixed embryo N2 DNase WS220 Basecalls were performed using CASAVA version 1.8. N2 input Paired End rep1 bd_0_1_2_6_ce10 UsingSRR GSM2339668 Embryo_mixed NA GSE87741 whole worms mixed embryo ERC09 DNase WS220 Basecalls were performed using CASAVA version 1.8. ERC09 input Paired End rep1 bd_0_1_2_6_ce10 UsingSRR GSM2339667 Embryo_mixed NA GSE87741 whole worms mixed embryo ERC08 DNase WS220 Basecalls were performed using CASAVA version 1.8. ERC08 input Paired End rep2 bd_0_1_2_6_ce10 UsingSRR GSM2339666 Embryo_mixed NA GSE87741 whole worms mixed embryo ERC08 DNase WS220 Basecalls were performed using CASAVA version 1.8. ERC08 input Paired End rep1 bd_0_1_2_6_ce10 UsingSRR GSM2339639 Embryo_mixed NA GSE87741 whole worms mixed embryo ERC51 DPY-27 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY27 ERC51 MxEmb rep3 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339638 Embryo_mixed NA GSE87741 whole worms mixed embryo ERC51 DPY-27 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY27 ERC51 MxEmb rep2 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339637 Embryo_mixed NA GSE87741 whole worms mixed embryo ERC51 DPY-27 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY27 ERC51 MxEmb rep1 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339636 Embryo_mixed NA GSE87741 whole worms mixed embryo ERC64 DPY-27 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY27 ERC64 MxEmb rep3 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339635 Embryo_mixed NA GSE87741 whole worms mixed embryo ERC64 DPY-27 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY27 ERC64 MxEmb rep2 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339634 Embryo_mixed NA GSE87741 whole worms mixed embryo ERC64 DPY-27 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY27 ERC64 MxEmb rep1 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339633 Embryo_mixed NA GSE87741 whole worms mixed embryo ERC54 DPY-27 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY27 ERC54 MxEmb rep2 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339632 Embryo_mixed NA GSE87741 whole worms mixed embryo ERC54 DPY-27 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY27 ERC54 MxEmb rep1 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339631 Embryo_mixed NA GSE87741 whole worms mixed embryo ERC38 SDC-3 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. SDC3 ERC38 MxEmb rep4 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339630 Embryo_mixed NA GSE87741 whole worms mixed embryo ERC38 SDC-3 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. SDC3 ERC38 MxEmb rep3 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339629 Embryo_mixed NA GSE87741 whole worms mixed embryo ERC38 SDC-3 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. SDC3 ERC38 MxEmb rep2 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339628 Embryo_mixed NA GSE87741 whole worms mixed embryo ERC38 SDC-3 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. SDC3 ERC38 MxEmb rep1 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339627 Embryo_mixed NA GSE87741 whole worms mixed embryo ERC38 DPY-27 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY27 ERC38 MxEmb rep3 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339626 Embryo_mixed NA GSE87741 whole worms mixed embryo ERC38 DPY-27 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY27 ERC38 MxEmb rep2 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339625 Embryo_mixed NA GSE87741 whole worms mixed embryo ERC38 DPY-27 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY27 ERC38 MxEmb rep1 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339624 Embryo_mixed NA GSE87741 whole worms mixed embryo TY1072 SDC-2 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. SDC2 TY1072 MxEmb rep3 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339623 Embryo_mixed NA GSE87741 whole worms mixed embryo TY1072 SDC-2 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. SDC2 TY1072 MxEmb rep2 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339622 Embryo_mixed NA GSE87741 whole worms mixed embryo TY1072 SDC-2 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. SDC2 TY1072 MxEmb rep1 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339621 Embryo_mixed NA GSE87741 whole worms mixed embryo TY2205 SDC-2 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. SDC2 TY2205 MxEmb rep2 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339612 Embryo_mixed NA GSE87741 whole worms mixed embryo N2 DPY-27 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY27 N2 MxEmb rep4 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339611 Embryo_mixed NA GSE87741 whole worms mixed embryo N2 DPY-27 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY27 N2 MxEmb rep3 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339610 Embryo_mixed NA GSE87741 whole worms mixed embryo N2 DPY-27 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY27 N2 MxEmb rep2 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339608 Embryo_mixed NA GSE87741 whole worms mixed embryo N2 DPY-30 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY30 N2 MxEmb rep5 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339607 Embryo_mixed NA GSE87741 whole worms mixed embryo N2 DPY-30 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY30 N2 MxEmb rep4 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339603 Embryo_mixed NA GSE87741 whole worms mixed embryo N2 SDC-3 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. SDC3 N2 MxEmb rep5 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339602 Embryo_mixed NA GSE87741 whole worms mixed embryo N2 SDC-3 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. SDC3 N2 MxEmb rep4 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339601 Embryo_mixed NA GSE87741 whole worms mixed embryo N2 SDC-3 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. SDC3 N2 MxEmb rep3 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339600 Embryo_mixed NA GSE87741 whole worms mixed embryo N2 SDC-3 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. SDC3 N2 MxEmb rep2 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339598 Embryo_mixed NA GSE87741 whole worms mixed embryo N2 SDC-2 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. SDC2 N2 MxEmb rep5 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339597 Embryo_mixed NA GSE87741 whole worms mixed embryo N2 SDC-2 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. SDC2 N2 MxEmb rep4 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2339596 Embryo_mixed NA GSE87741 whole worms mixed embryo N2 SDC-2 ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. SDC2 N2 MxEmb rep3 ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM2098451 Embryo_mixed NA GSE79567 Embryo Mixed-stage N2 MNase ce10 Paired end reads were mapped to ce10 genome release using Bowtie (v1.1.2) with stringent multimapping parameters: bowtie -q -X 2000 --fr -p 1 -S -n 2 -e 70 -l 28 --pairtries 100 --maxbts 125 -k 1 -m 1 --un /Unmapped_Reads.fastq --phred33-quals /ce10 -1 /read1.fastq -2 /read2.fastq HS rep2 - 2m_MNase-seq bd_0_1_2_non_ce10 GSM2098451_HS_rep2_MNaseTC_2m_calledNucleosomes.bed.gz GSM2098445 Embryo_mixed NA GSE79567 Embryo Mixed-stage N2 MNase ce10 Paired end reads were mapped to ce10 genome release using Bowtie (v1.1.2) with stringent multimapping parameters: bowtie -q -X 2000 --fr -p 1 -S -n 2 -e 70 -l 28 --pairtries 100 --maxbts 125 -k 1 -m 1 --un /Unmapped_Reads.fastq --phred33-quals /ce10 -1 /read1.fastq -2 /read2.fastq HS rep1 - 2m_MNase-seq bd_0_1_2_non_ce10 GSM2098445_HS_rep1_MNaseTC_2m_calledNucleosomes.bed.gz GSM2098439 Embryo_mixed NA GSE79567 Embryo Mixed-stage N2 MNase ce10 Paired end reads were mapped to ce10 genome release using Bowtie (v1.1.2) with stringent multimapping parameters: bowtie -q -X 2000 --fr -p 1 -S -n 2 -e 70 -l 28 --pairtries 100 --maxbts 125 -k 1 -m 1 --un /Unmapped_Reads.fastq --phred33-quals /ce10 -1 /read1.fastq -2 /read2.fastq RT rep2 - 2m_MNase-seq bd_0_1_2_non_ce10 GSM2098439_RT_rep2_MNaseTC_2m_calledNucleosomes.bed.gz GSM2098433 Embryo_mixed NA GSE79567 Embryo Mixed-stage N2 MNase ce10 Paired end reads were mapped to ce10 genome release using Bowtie (v1.1.2) with stringent multimapping parameters: bowtie -q -X 2000 --fr -p 1 -S -n 2 -e 70 -l 28 --pairtries 100 --maxbts 125 -k 1 -m 1 --un /Unmapped_Reads.fastq --phred33-quals /ce10 -1 /read1.fastq -2 /read2.fastq RT rep1 - 2m_MNase-seq bd_0_1_2_non_ce10 GSM2098433_RT_rep1_MNaseTC_2m_calledNucleosomes.bed.gz GSM1048406 Embryo_mixed NA GSE50488 Mixed-stage embryos N2 SDQ2358_AMA1 ChIP-Seq ce6 Unique sequencing reads were aligned to the C. elegans reference genome (ce6, WS190) using bowtie, allowing up to two mismatches BC216 [ChIP-Seq] bw_0_1_2_4_ce6 GSM1048406.bigwig GSM1048405 Embryo_mixed NA GSE50488 Mixed-stage embryos N2 SDQ2357_AMA1 ChIP-Seq ce6 Unique sequencing reads were aligned to the C. elegans reference genome (ce6, WS190) using bowtie, allowing up to two mismatches BC176 [ChIP-Seq] bw_0_1_2_4_ce6 GSM1048405.bigwig GSM1048404 Embryo_mixed NA GSE50488 Mixed-stage embryos N2 SDQ2358_AMA1 ChIP-Seq ce6 Unique sequencing reads were aligned to the C. elegans reference genome (ce6, WS190) using bowtie, allowing up to two mismatches BC215 [ChIP-Seq] bw_0_1_2_4_ce6 GSM1048404.bigwig GSM1048403 Embryo_mixed NA GSE50488 Mixed-stage embryos N2 SDQ2357_AMA1 ChIP-Seq ce6 Unique sequencing reads were aligned to the C. elegans reference genome (ce6, WS190) using bowtie, allowing up to two mismatches BC175 [ChIP-Seq] bw_0_1_2_4_ce6 GSM1048403.bigwig GSM1048423 Embryo_mixed NA GSE42741 Mixed-stage embryos N2 SDQ0839_TBP1 ChIP-Seq ce6 Unique sequencing reads were aligned to the C. elegans reference genome (ce6, WS190) using bowtie, allowing up to two mismatches TBP-1 ChIP-seq in N2 mixed-stage embryos treated with NPP-13 RNAi (BC258) bw_0_1_2_4_ce6 GSM1048423.bigwig GSM1048422 Embryo_mixed NA GSE42741 Mixed-stage embryos N2 SDQ0839_TBP1 ChIP-Seq ce6 Unique sequencing reads were aligned to the C. elegans reference genome (ce6, WS190) using bowtie, allowing up to two mismatches TBP-1 ChIP-seq in N2 mixed-stage embryos treated with empty vector (BC257) bw_0_1_2_4_ce6 GSM1048422.bigwig GSM1048421 Embryo_mixed NA GSE42741 Mixed-stage embryos N2 SDQ0839_TBP1 ChIP-Seq ce6 Unique sequencing reads were aligned to the C. elegans reference genome (ce6, WS190) using bowtie, allowing up to two mismatches TBP-1 ChIP-seq in N2 mixed-stage embryos (BC057) bw_0_1_2_4_ce6 GSM1048421.bigwig GSM1048420 Embryo_mixed NA GSE42741 Mixed-stage embryos N2 POLR2A ChIP-Seq ce6 Unique sequencing reads were aligned to the C. elegans reference genome (ce6, WS190) using bowtie, allowing up to two mismatches Pol III RPC-1 ChIP-seq in N2 mixed-stage embryos treated with NPP-13 RNAi (BC180) bw_0_1_2_4_ce6 GSM1048420.bigwig GSM1048419 Embryo_mixed NA GSE42741 Mixed-stage embryos N2 POLR2A ChIP-Seq ce6 Unique sequencing reads were aligned to the C. elegans reference genome (ce6, WS190) using bowtie, allowing up to two mismatches Pol III RPC-1 ChIP-seq in N2 mixed-stage embryos treated with empty vector (BC179) bw_0_1_2_4_ce6 GSM1048419.bigwig GSM1048418 Embryo_mixed NA GSE42741 Mixed-stage embryos N2 POLR2A ChIP-Seq ce6 Unique sequencing reads were aligned to the C. elegans reference genome (ce6, WS190) using bowtie, allowing up to two mismatches Pol III RPC-1 ChIP-seq in N2 mixed-stage embryos treated with NPP-13 RNAi (BC178) bw_0_1_2_4_ce6 GSM1048418.bigwig GSM1048417 Embryo_mixed NA GSE42741 Mixed-stage embryos N2 POLR2A ChIP-Seq ce6 Unique sequencing reads were aligned to the C. elegans reference genome (ce6, WS190) using bowtie, allowing up to two mismatches Pol III RPC-1 ChIP-seq in N2 mixed-stage embryos treated with empty vector (BC177) bw_0_1_2_4_ce6 GSM1048417.bigwig GSM1048416 Embryo_mixed NA GSE42741 Mixed-stage embryos N2 SY1539_NPP3 ChIP-Seq ce6 Unique sequencing reads were aligned to the C. elegans reference genome (ce6, WS190) using bowtie, allowing up to two mismatches NPP-3 ChIP-seq in N2 mixed-stage embryos (BC164) bw_0_1_2_4_ce6 GSM1048416.bigwig GSM1048415 Embryo_mixed NA GSE42741 Mixed-stage embryos N2 SY1540_NPP3 ChIP-Seq ce6 Unique sequencing reads were aligned to the C. elegans reference genome (ce6, WS190) using bowtie, allowing up to two mismatches NPP-3 ChIP-seq in N2 mixed-stage embryos (BC076) bw_0_1_2_4_ce6 GSM1048415.bigwig GSM1048414 Embryo_mixed NA GSE42741 Mixed-stage embryos N2 SY1539_NPP3 ChIP-Seq ce6 Unique sequencing reads were aligned to the C. elegans reference genome (ce6, WS190) using bowtie, allowing up to two mismatches NPP-3 ChIP-seq in N2 mixed-stage embryos (BC075) bw_0_1_2_4_ce6 GSM1048414.bigwig GSM1048413 Embryo_mixed NA GSE42741 Mixed-stage embryos N2 SDQ3897_NPP13 ChIP-Seq ce6 Unique sequencing reads were aligned to the C. elegans reference genome (ce6, WS190) using bowtie, allowing up to two mismatches NPP-13 ChIP-seq in N2 mixed-stage embryos (KI024) bw_0_1_2_4_ce6 GSM1048413.bigwig GSM1048409 Embryo_mixed NA GSE42741 Mixed-stage embryos N2 SDQ4154_IMB1 ChIP-Seq ce6 Unique sequencing reads were aligned to the C. elegans reference genome (ce6, WS190) using bowtie, allowing up to two mismatches IMB-1 ChIP-seq in N2 mixed-stage embryos (BC166) bw_0_1_2_4_ce6 GSM1048409.bigwig GSM1048402 Embryo_mixed NA GSE42741 Mixed-stage embryos N2 SDQ2357_AMA1 ChIP-Seq ce6 Unique sequencing reads were aligned to the C. elegans reference genome (ce6, WS190) using bowtie, allowing up to two mismatches AMA-1 ChIP-seq in N2 mixed-stage embryos (BC002) bw_0_1_2_4_ce6 GSM1048402.bigwig GSM1048401 Embryo_mixed NA GSE42741 Mixed-stage embryos N2 SDQ2357_AMA1 ChIP-Seq ce6 Unique sequencing reads were aligned to the C. elegans reference genome (ce6, WS190) using bowtie, allowing up to two mismatches AMA-1 ChIP-seq in N2 mixed-stage embryos (BC085) bw_0_1_2_4_ce6 GSM1048401.bigwig GSM1048424 Embryo_mixed NA GSE42741 Mixed-stage embryos N2 SDQ0839_TBP1 ChIP-Seq ce6 Unique sequencing reads were aligned to the C. elegans reference genome (ce6, WS190) using bowtie, allowing up to two mismatches TBP-1 ChIP-seq in N2 mixed-stage embryos (FW002) bw_0_1_2_4_ce6 GSM1048424.bigwig GSM1048410 Embryo_mixed NA GSE42741 Mixed-stage embryos N2 SDQ4154_IMB1 ChIP-Seq ce6 Unique sequencing reads were aligned to the C. elegans reference genome (ce6, WS190) using bowtie, allowing up to two mismatches IMB-1 ChIP-seq in N2 mixed-stage embryos (KI026) bw_0_1_2_4_ce6 GSM1048410.bigwig GSM1217516 Embryo_mixed NA GSE50328 seq-SDQ4640_SWD3_N2_Mxemb_ChIP_Rep2 Mixed Embryo N2 seq-SDQ4640_SWD3_N2_Mxemb_ChIP ChIP-Seq ce10 DNA was blunt-ended with End Repair Enzyme mix (Epicentre, Madison) and A-overhanged with Exo(-) Klenow fragment in the presence of dATP. DNA fragments were ligated with adaptors. DNA was amplified by PCR with single-end or pair-end primers. Amplicon was loaded on an agarose gel, and DNA at an indicated size range was recovered from the gel. seq-SDQ4640_SWD3_N2_Mxemb_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217516_seq-SDQ4640_SWD3_N2_MXemb_2_A_EE13_BC049_peaks.GFF3.gz GSM1217515 Embryo_mixed NA GSE50328 seq-SDQ4640_SWD3_N2_Mxemb_ChIP_Rep1 Mixed Embryo N2 seq-SDQ4640_SWD3_N2_Mxemb_ChIP ChIP-Seq ce10 DNA was blunt-ended with End Repair Enzyme mix (Epicentre, Madison) and A-overhanged with Exo(-) Klenow fragment in the presence of dATP. DNA fragments were ligated with adaptors. DNA was amplified by PCR with single-end or pair-end primers. Amplicon was loaded on an agarose gel, and DNA at an indicated size range was recovered from the gel. seq-SDQ4640_SWD3_N2_Mxemb_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217515_seq-SDQ4640_SWD3_N2_MXemb_1_A_EE9_BC018_peaks.GFF3.gz GSM1217512 Embryo_mixed NA GSE50327 seq-SDQ4585_ASH2_N2_Mxemb_ChIP_Rep2 Mixed Embryo N2 seq-SDQ4585_ASH2_N2_Mxemb_ChIP ChIP-Seq ce10 DNA was blunt-ended with End Repair Enzyme mix (Epicentre, Madison) and A-overhanged with Exo(-) Klenow fragment in the presence of dATP. DNA fragments were ligated with adaptors. DNA was amplified by PCR with single-end or pair-end primers. Amplicon was loaded on an agarose gel, and DNA at an indicated size range was recovered from the gel. seq-SDQ4585_ASH2_N2_Mxemb_ChIP_Rep2 bd_0_1_2_6_ce10 UsingSRR GSM1217511 Embryo_mixed NA GSE50327 seq-SDQ4585_ASH2_N2_Mxemb_ChIP_Rep1 Mixed Embryo N2 seq-SDQ4585_ASH2_N2_Mxemb_ChIP ChIP-Seq ce10 DNA was blunt-ended with End Repair Enzyme mix (Epicentre, Madison) and A-overhanged with Exo(-) Klenow fragment in the presence of dATP. DNA fragments were ligated with adaptors. DNA was amplified by PCR with single-end or pair-end primers. Amplicon was loaded on an agarose gel, and DNA at an indicated size range was recovered from the gel. seq-SDQ4585_ASH2_N2_Mxemb_ChIP_Rep1 bd_0_1_2_6_ce10 UsingSRR GSM1217508 Embryo_mixed NA GSE50326 seq-SDQ4564_DPY28_N2_Mxemb_ChIP_Rep2 Mixed Embryo N2 seq-SDQ4564_DPY28_N2_Mxemb_ChIP ChIP-Seq ce10 DNA was blunt-ended with End Repair Enzyme mix (Epicentre, Madison) and A-overhanged with Exo(-) Klenow fragment in the presence of dATP. DNA fragments were ligated with adaptors. DNA was amplified by PCR with single-end or pair-end primers. Amplicon was loaded on an agarose gel, and DNA at an indicated size range was recovered from the gel. seq-SDQ4564_DPY28_N2_Mxemb_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217508_seq-SDQ4564_DPY28_N2_MXemb_2_A_EE13_BC037_peaks.GFF3.gz GSM1217507 Embryo_mixed NA GSE50326 seq-SDQ4564_DPY28_N2_Mxemb_ChIP_Rep1 Mixed Embryo N2 seq-SDQ4564_DPY28_N2_Mxemb_ChIP ChIP-Seq ce10 DNA was blunt-ended with End Repair Enzyme mix (Epicentre, Madison) and A-overhanged with Exo(-) Klenow fragment in the presence of dATP. DNA fragments were ligated with adaptors. DNA was amplified by PCR with single-end or pair-end primers. Amplicon was loaded on an agarose gel, and DNA at an indicated size range was recovered from the gel. seq-SDQ4564_DPY28_N2_Mxemb_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217507_seq-SDQ4564_DPY28_N2_MXemb_1_A_EE9_BC023_peaks.GFF3.gz GSM1217504 Embryo_mixed NA GSE50325 seq-SDQ4562_SMC6_N2_Mxemb_ChIP_Rep2 Mixed Embryo N2 seq-SDQ4562_SMC6_N2_Mxemb_ChIP ChIP-Seq ce10 DNA was blunt-ended with End Repair Enzyme mix (Epicentre, Madison) and A-overhanged with Exo(-) Klenow fragment in the presence of dATP. DNA fragments were ligated with adaptors. DNA was amplified by PCR with single-end or pair-end primers. Amplicon was loaded on an agarose gel, and DNA at an indicated size range was recovered from the gel. seq-SDQ4562_SMC6_N2_Mxemb_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217504_seq-SDQ4562_SMC6_N2_MXemb_2_A_EE13_BC042_peaks.GFF3.gz GSM1217503 Embryo_mixed NA GSE50325 seq-SDQ4562_SMC6_N2_Mxemb_ChIP_Rep1 Mixed Embryo N2 seq-SDQ4562_SMC6_N2_Mxemb_ChIP ChIP-Seq ce10 DNA was blunt-ended with End Repair Enzyme mix (Epicentre, Madison) and A-overhanged with Exo(-) Klenow fragment in the presence of dATP. DNA fragments were ligated with adaptors. DNA was amplified by PCR with single-end or pair-end primers. Amplicon was loaded on an agarose gel, and DNA at an indicated size range was recovered from the gel. seq-SDQ4562_SMC6_N2_Mxemb_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217503_seq-SDQ4562_SMC6_N2_MXemb_1_A_EE9_BC022_peaks.GFF3.gz GSM1217496 Embryo_mixed NA GSE50323 seq-SDQ4561_DPY26_N2_Mxemb_ChIP_Rep2 Mixed Embryo N2 seq-SDQ4561_DPY26_N2_Mxemb_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ4561_DPY26_N2_Mxemb_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217496_BC092_peaks.GFF3.gz GSM1217495 Embryo_mixed NA GSE50323 seq-SDQ4561_DPY26_N2_Mxemb_ChIP_Rep1 Mixed Embryo N2 seq-SDQ4561_DPY26_N2_Mxemb_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ4561_DPY26_N2_Mxemb_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217495_seq-SDQ4561_DPY26_N2_MXemb_1_A_EE14_BC068_peaks.GFF3.gz GSM1217480 Embryo_mixed NA GSE50319 seq-SDQ4496_DPY26_N2_Mxemb_ChIP_Rep2 Mixed Embryo N2 seq-SDQ4496_DPY26_N2_Mxemb_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ4496_DPY26_N2_Mxemb_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217480_BC093_peaks.GFF3.gz GSM1217479 Embryo_mixed NA GSE50319 seq-SDQ4496_DPY26_N2_Mxemb_ChIP_Rep1 Mixed Embryo N2 seq-SDQ4496_DPY26_N2_Mxemb_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ4496_DPY26_N2_Mxemb_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217479_seq-SDQ4496_DPY26_N2_MXemb_1_A_EE14_BC067_peaks.GFF3.gz GSM1217476 Embryo_mixed NA GSE50318 seq-SDQ4493_MAU2_N2_Mxemb_ChIP_Rep2 Mixed Embryo N2 seq-SDQ4493_MAU2_N2_Mxemb_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ4493_MAU2_N2_Mxemb_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217476_BC091_peaks.GFF3.gz GSM1217475 Embryo_mixed NA GSE50318 seq-SDQ4493_MAU2_N2_Mxemb_ChIP_Rep1 Mixed Embryo N2 seq-SDQ4493_MAU2_N2_Mxemb_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ4493_MAU2_N2_Mxemb_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217475_seq-SDQ4493-MAU2_N2_MXemb_1_A_EE13_BC033_peaks.GFF3.gz GSM1217472 Embryo_mixed NA GSE50317 seq-SDQ4481_PQN85_N2_Mxemb_ChIP_Rep2 Mixed Embryo N2 seq-SDQ4481_PQN85_N2_Mxemb_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ4481_PQN85_N2_Mxemb_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217472_BC072_peaks.GFF3.gz GSM1217471 Embryo_mixed NA GSE50317 seq-SDQ4481_PQN85_N2_Mxemb_ChIP_Rep1 Mixed Embryo N2 seq-SDQ4481_PQN85_N2_Mxemb_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ4481_PQN85_N2_Mxemb_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217471_seq-SDQ4481-PQN85_N2_MXemb_1_A_EE13_BC047_peaks.GFF3.gz GSM1217468 Embryo_mixed NA GSE50316 seq-SDQ4154_IMB1_N2_Mxemb_ChIP_Rep2 Mixed Embryo N2 seq-SDQ4154_IMB1_N2_Mxemb_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ4154_IMB1_N2_Mxemb_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217468_KI026_peaks.GFF3.gz GSM1217467 Embryo_mixed NA GSE50316 seq-SDQ4154_IMB1_N2_Mxemb_ChIP_Rep1 Mixed Embryo N2 seq-SDQ4154_IMB1_N2_Mxemb_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ4154_IMB1_N2_Mxemb_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217467_BC166_peaks.GFF3.gz GSM1217456 Embryo_mixed NA GSE50313 seq-SDQ4109_TAF1_N2_Mxemb_ChIP_Rep2 Mixed Embryo N2 seq-SDQ4109_TAF1_N2_Mxemb_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ4109_TAF1_N2_Mxemb_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217456_FW001_01458_001_UNCCH_100422_UNC4-RDR3001561_0002_3_peaks.GFF3.gz GSM1217455 Embryo_mixed NA GSE50313 seq-SDQ4109_TAF1_N2_Mxemb_ChIP_Rep1 Mixed Embryo N2 seq-SDQ4109_TAF1_N2_Mxemb_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ4109_TAF1_N2_Mxemb_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217455_seq-SDQ4109_TAF1_N2_MXemb_2_A_EE13_BC056_peaks.GFF3.gz GSM1217444 Embryo_mixed NA GSE50310 seq-SDQ3892_MIX1_N2_Mxemb_ChIP_Rep2 Mixed Embryo N2 seq-SDQ3892_MIX1_N2_Mxemb_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3892_MIX1_N2_Mxemb_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217444_BC073_peaks.GFF3.gz GSM1217443 Embryo_mixed NA GSE50310 seq-SDQ3892_MIX1_N2_Mxemb_ChIP_Rep1 Mixed Embryo N2 seq-SDQ3892_MIX1_N2_Mxemb_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3892_MIX1_N2_Mxemb_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217443_seq-SDQ3892_MIX1_N2_MXemb_1_A_EE13_BC030_peaks.GFF3.gz GSM1217440 Embryo_mixed NA GSE50309 seq-SDQ3856_SDC1_N2_Mxemb_ChIP_Rep2 Mixed Embryo N2 seq-SDQ3856_SDC1_N2_Mxemb_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3856_SDC1_N2_Mxemb_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217440_BC094_peaks.GFF3.gz GSM1217439 Embryo_mixed NA GSE50309 seq-SDQ3856_SDC1_N2_Mxemb_ChIP_Rep1 Mixed Embryo N2 seq-SDQ3856_SDC1_N2_Mxemb_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3856_SDC1_N2_Mxemb_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217439_BC070_peaks.GFF3.gz GSM1217436 Embryo_mixed NA GSE50308 seq-SDQ3582_CBP1_N2_Mxemb_ChIP_Rep2 Mixed Embryo N2 seq-SDQ3582_CBP1_N2_Mxemb_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3582_CBP1_N2_Mxemb_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217436_KI22_peaks.GFF3.gz GSM1217435 Embryo_mixed NA GSE50308 seq-SDQ3582_CBP1_N2_Mxemb_ChIP_Rep1 Mixed Embryo N2 seq-SDQ3582_CBP1_N2_Mxemb_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ3582_CBP1_N2_Mxemb_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217435_BC053_peaks.GFF3.gz GSM1217432 Embryo_mixed NA GSE50307 seq-SDQ3499_DPY30_N2_Mxemb_ChIP_Rep2 Mixed Embryo N2 seq-SDQ3499_DPY30_N2_Mxemb_ChIP ChIP-Seq ce10 DNA was blunt-ended with End Repair Enzyme mix (Epicentre, Madison) and A-overhanged with Exo(-) Klenow fragment in the presence of dATP. DNA fragments were ligated with adaptors. DNA was amplified by PCR with single-end or pair-end primers. Amplicon was loaded on an agarose gel, and DNA at an indicated size range was recovered from the gel. seq-SDQ3499_DPY30_N2_Mxemb_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217432_BC086_peaks.GFF3.gz GSM1217431 Embryo_mixed NA GSE50307 seq-SDQ3499_DPY30_N2_Mxemb_ChIP_Rep1 Mixed Embryo N2 seq-SDQ3499_DPY30_N2_Mxemb_ChIP ChIP-Seq ce10 DNA was blunt-ended with End Repair Enzyme mix (Epicentre, Madison) and A-overhanged with Exo(-) Klenow fragment in the presence of dATP. DNA fragments were ligated with adaptors. DNA was amplified by PCR with single-end or pair-end primers. Amplicon was loaded on an agarose gel, and DNA at an indicated size range was recovered from the gel. seq-SDQ3499_DPY30_N2_Mxemb_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217431_BC003_peaks.GFF3.gz GSM1217428 Embryo_mixed NA GSE50306 seq-SDQ2357Q2358_AMA1_N2_Mxemb_RiIMB1_ChIP_Rep2 Mixed Embryo N2 seq-SDQ2357Q2358_AMA1_N2_Mxemb_RiIMB1_ChIP ChIP-Seq ce10 Worms were cultured in liquid S-medium with HB101 bacteria for 36 hrs (L3-L4 stage). Washed L3-L4 worms were transferred to new S-medium supplemented with IPTG-induced RNAi bacteria. Gravid worms were harvested and bleached to obtain embryos. seq-SDQ2357Q2358_AMA1_N2_Mxemb_RiIMB1_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217428_BC218_peaks.GFF3.gz GSM1217427 Embryo_mixed NA GSE50306 seq-SDQ2357Q2358_AMA1_N2_Mxemb_RiIMB1_ChIP_Rep1 Mixed Embryo N2 seq-SDQ2357Q2358_AMA1_N2_Mxemb_RiIMB1_ChIP ChIP-Seq ce10 Worms were cultured in liquid S-medium with HB101 bacteria for 36 hrs (L3-L4 stage). Washed L3-L4 worms were transferred to new S-medium supplemented with IPTG-induced RNAi bacteria. Gravid worms were harvested and bleached to obtain embryos. seq-SDQ2357Q2358_AMA1_N2_Mxemb_RiIMB1_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217427_BC217_peaks.GFF3.gz GSM1217424 Embryo_mixed NA GSE50305 seq-SDQ2357Q2358_AMA1_N2_Mxemb_EE_ChIP_Rep2 Mixed Embryo N2 seq-SDQ2357Q2358_AMA1_N2_Mxemb_EE_ChIP ChIP-Seq ce10 DNA was blunt-ended with End Repair Enzyme mix (Epicentre, Madison) and A-overhanged with Exo(-) Klenow fragment in the presence of dATP. DNA fragments were ligated with adaptors. DNA was amplified by PCR with single-end or pair-end primers. Amplicon was loaded on an agarose gel, and DNA at an indicated size range was recovered from the gel. seq-SDQ2357Q2358_AMA1_N2_Mxemb_EE_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217424_BC085_peaks.GFF3.gz GSM1217423 Embryo_mixed NA GSE50305 seq-SDQ2357Q2358_AMA1_N2_Mxemb_EE_ChIP_Rep1 Mixed Embryo N2 seq-SDQ2357Q2358_AMA1_N2_Mxemb_EE_ChIP ChIP-Seq ce10 DNA was blunt-ended with End Repair Enzyme mix (Epicentre, Madison) and A-overhanged with Exo(-) Klenow fragment in the presence of dATP. DNA fragments were ligated with adaptors. DNA was amplified by PCR with single-end or pair-end primers. Amplicon was loaded on an agarose gel, and DNA at an indicated size range was recovered from the gel. seq-SDQ2357Q2358_AMA1_N2_Mxemb_EE_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217423_BC002_peaks.GFF3.gz GSM1217420 Embryo_mixed NA GSE50304 seq-SDQ0839_TBP1_N2_Mxemb_EE_ChIP_Rep2 Mixed Embryo N2 seq-SDQ0839_TBP1_N2_Mxemb_EE_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ0839_TBP1_N2_Mxemb_EE_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217420_FW002_peaks.GFF3.gz GSM1217419 Embryo_mixed NA GSE50304 seq-SDQ0839_TBP1_N2_Mxemb_EE_ChIP_Rep1 Mixed Embryo N2 seq-SDQ0839_TBP1_N2_Mxemb_EE_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ0839_TBP1_N2_Mxemb_EE_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217419_seq-SDQ0839_TBP1_N2_MXemb_2_A_EE13_BC057_peaks.GFF3.gz GSM1217416 Embryo_mixed NA GSE50303 seq-OD0039_SMC4_N2_Mxemb_ChIP_Rep2 Mixed Embryo N2 seq-OD0039_SMC4_N2_Mxemb_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-OD0039_SMC4_N2_Mxemb_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217416_SE128_peaks.GFF3.gz GSM1217415 Embryo_mixed NA GSE50303 seq-OD0039_SMC4_N2_Mxemb_ChIP_Rep1 Mixed Embryo N2 seq-OD0039_SMC4_N2_Mxemb_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-OD0039_SMC4_N2_Mxemb_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217415_SE125_peaks.GFF3.gz GSM1217412 Embryo_mixed NA GSE50302 seq-NBP170893_HTZ1_N2_Mxemb_ChIP_Rep2 Mixed Embryo N2 seq-NBP170893_HTZ1_N2_Mxemb_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-NBP170893_HTZ1_N2_Mxemb_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1217412_BC167_peaks.GFF3.gz GSM1217411 Embryo_mixed NA GSE50302 seq-NBP170893_HTZ1_N2_Mxemb_ChIP_Rep1 Mixed Embryo N2 seq-NBP170893_HTZ1_N2_Mxemb_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-NBP170893_HTZ1_N2_Mxemb_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1217411_BC077_peaks.GFF3.gz GSM1206417 Embryo_mixed NA GSE49751 seq-SDQ2946_HCP4_N2_Mxemb_ChIP_Rep2 Mixed Embryo N2 seq-SDQ2946_HCP4_N2_Mxemb_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ2946_HCP4_N2_Mxemb_ChIP_Rep2 bd_0_3_4_5_ce10 GSM1206417_BC267_peaks.GFF3.gz GSM1206416 Embryo_mixed NA GSE49751 seq-SDQ2946_HCP4_N2_Mxemb_ChIP_Rep1 Mixed Embryo N2 seq-SDQ2946_HCP4_N2_Mxemb_ChIP ChIP-Seq ce10 ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM seq-SDQ2946_HCP4_N2_Mxemb_ChIP_Rep1 bd_0_3_4_5_ce10 GSM1206416_BC191_peaks.GFF3.gz GSM514735 Embryo_mixed NA GSE20136 mixed stage embryos embryo N2 MNase-Seq WS170 Raw coverage tracks: The sequencing was done using Illumina paired end reads technology. All lanes of each replicate were combined and mapped together. The two single reads of each pair were mapped independently to WS170 genome, using a proprietary software (SeqHit) allowing a single mismatch and no gaps. The hits of the non unique reads were extended to a nucleosomes length and their union defined the non unique regions. The pairs of mapped reads that define a valid (up to 200 basepairs length) and unique regions are collected. The raw coverage of a basepair is caluclated by summing up the number of unique reads covering it. Zero value is assigned to unique basepairs that were covered by none. embryo_mononuc_seq bw_0_1_2_4_ce4 GSM514735.bigwig