Chromatin accessibility is a two-tier process regulated by transcription factor pioneering and enhancer activation

The supporting files to this publication are as follows:

Mapped motif instances from ZDTBCG BPNet model trained on ChIP-nexus data (dm6): all_instances_curated_0based.bed

Trained model files used for downstream interpretation:

• ZDTBCG_model.h5: BPNet model trained on Zelda, Dorsal, Twist, Bicoid, Caudal and GAGA-factor ChIP-nexus in 2-3hr Drosophila OreR embryos
• bias_model_thresh_5.h5: ChromBPNet bias model trained on low-count, non-peak regions of ATAC-seq for 2.5-3hr Drosophila OreR embryos
• model_fold1_1to15.h5: ChromBPNet bias model trained on consolidated peak regions across all ATAC-seq timepoints, trained to predict ATAC-seq data in 1-1.5hr Drosophila OreR embryos.
• model_fold1_15to2.h5: ChromBPNet bias model trained on consolidated peak regions across all ATAC-seq timepoints, trained to predict ATAC-seq data in 1.5-2hr Drosophila OreR embryos.
• model_fold1_2to25.h5: ChromBPNet bias model trained on consolidated peak regions across all ATAC-seq timepoints, trained to predict ATAC-seq data in 2-2.5hr Drosophila OreR embryos.
• model_fold1_25to3.h5: ChromBPNet bias model trained on consolidated peak regions across all ATAC-seq timepoints, trained to predict ATAC-seq data in 2.5-3hr Drosophila OreR embryos.

Output model predictions of ChIP-nexus and ATAC-seq coverage across trained genomic regions:

• Bcd.preds.neg.bw: Bicoid negative strand BPNet prediction of ChIP-nexus coverage across trained regions for the ZDTBCG model.
• Bcd.preds.pos.bw: Bicoid positive strand BPNet prediction of ChIP-nexus coverage across trained regions for the ZDTBCG model.
• Cad.preds.neg.bw: Caudal negative strand BPNet prediction of ChIP-nexus coverage across trained regions for the ZDTBCG model.
• Cad.preds.pos.bw: Caudal positive strand BPNet prediction of ChIP-nexus coverage across trained regions for the ZDTBCG model.
• Dl.preds.neg.bw: Dorsal negative strand BPNet prediction of ChIP-nexus coverage across trained regions for the ZDTBCG model.
• Dl.preds.pos.bw: Dorsal positive strand BPNet prediction of ChIP-nexus coverage across trained regions for the ZDTBCG model.
• Twi.preds.neg.bw: Twist negative strand BPNet prediction of ChIP-nexus coverage across trained regions for the ZDTBCG model.
• Twi.preds.pos.bw: Twist positive strand BPNet prediction of ChIP-nexus coverage across trained regions for the ZDTBCG model.
• Zld.preds.neg.bw: Zelda negative strand BPNet prediction of ChIP-nexus coverage across trained regions for the ZDTBCG model.
• Zld.preds.pos.bw: Zelda positive strand BPNet prediction of ChIP-nexus coverage across trained regions for the ZDTBCG model.
• GAF.preds.neg.bw: GAGA-factor negative strand BPNet prediction of ChIP-nexus coverage across trained regions for the ZDTBCG model.
• GAF.preds.pos.bw: GAGA-factor positive strand BPNet prediction of ChIP-nexus coverage across trained regions for the ZDTBCG model.
• preds_fold1_1to15_wo_bias.bw: ChromBPNet prediction of ATAC-seq coverage with the Tn5 bias removed for 1-1.5hr Drosophila OreR embryos.
• preds_fold1_15to2_wo_bias.bw: ChromBPNet prediction of ATAC-seq coverage with the Tn5 bias removed for 1.5-2hr Drosophila OreR embryos.
• preds_fold1_2to25_wo_bias.bw: ChromBPNet prediction of ATAC-seq coverage with the Tn5 bias removed for 2-2.5hr Drosophila OreR embryos.
• preds_fold1_25to3_wo_bias.bw: ChromBPNet prediction of ATAC-seq coverage with the Tn5 bias removed for 2.5-3hr Drosophila OreR embryos.

Output DeepLIFT/SHAP predictions of contribution scores for BPNet and ChromBPNet models across trained genomic regions:

• Bcd.contrib.counts.bw: Bicoid counts contribution for ChIP-nexus across trained regions for the ZDTBCG BPNet model.
• Bcd.contrib.profile.bw: Bicoid profile contribution for ChIP-nexus across trained regions for the ZDTBCG BPNet model.
• Cad.contrib.counts.bw: Caudal counts contribution for ChIP-nexus across trained regions for the ZDTBCG BPNet model.
• Cad.contrib.profile.bw: Caudal profile contribution for ChIP-nexus across trained regions for the ZDTBCG BPNet model.
• Dl.contrib.counts.bw: Dorsal counts contribution for ChIP-nexus across trained regions for the ZDTBCG BPNet model.
• Dl.contrib.profile.bw: Dorsal profile contribution for ChIP-nexus across trained regions for the ZDTBCG BPNet model.
• Twi.contrib.counts.bw: Twist counts contribution for ChIP-nexus across trained regions for the ZDTBCG BPNet model.
• Twi.contrib.profile.bw: Twist profile contribution for ChIP-nexus across trained regions for the ZDTBCG BPNet model.
• Zld.contrib.counts.bw: Zelda counts contribution for ChIP-nexus across trained regions for the ZDTBCG BPNet model.
• Zld.contrib.profile.bw: Zelda profile contribution for ChIP-nexus across trained regions for the ZDTBCG BPNet model.
• GAF.contrib.counts.bw: GAGA-factor counts contribution for ChIP-nexus across trained regions for the ZDTBCG BPNet model.
• GAF.contrib.profile.bw: GAGA-factor profile contribution for ChIP-nexus across trained regions for the ZDTBCG BPNet model.
• preds_fold1_1to15.counts_scores.bw: Counts contribution for ATAC-seq across trained regions for the ChromBPNet model trained on 1-1.5hr Drosophila OreR embryos.
• preds_fold1_1to15.profile_scores.bw: Profile contribution for ATAC-seq across trained regions for the ChromBPNet model trained on 1-1.5hr Drosophila OreR embryos.
• preds_fold1_15to2.counts_scores.bw: Counts contribution for ATAC-seq across trained regions for the ChromBPNet model trained on 1.5-2hr Drosophila OreR embryos.
• preds_fold1_15to2..profile_scores.bw: Profile contribution for ATAC-seq across trained regions for the ChromBPNet model trained on 1.5-2hr Drosophila OreR embryos.
• preds_fold1_2to25.counts_scores.bw: Counts contribution for ATAC-seq across trained regions for the ChromBPNet model trained on 2-2.5hr Drosophila OreR embryos.
• preds_fold1_2to25.profile_scores.bw: Profile contribution for ATAC-seq across trained regions for the ChromBPNet model trained on 2-2.5hr Drosophila OreR embryos.
• preds_fold1_25to3.counts_scores.bw: Counts contribution for ATAC-seq across trained regions for the ChromBPNet model trained on 2.5-3hr Drosophila OreR embryos.
• preds_fold1_25to3.profile_scores.bw: Profile contribution for ATAC-seq across trained regions for the ChromBPNet model trained on 2.5-3hr Drosophila OreR embryos.

Experimental pooled ChIP-nexus and ATAC-seq cutsite coverage:

• orer_bcd_mbt_nexus_combined_normalized_negative.bw: Reads-per-million normalized ChIP-nexus negative strand pooled coverage of Bicoid across 2-3hr Drosophila OreR embryos
• orer_bcd_mbt_nexus_combined_normalized_positive.bw: Reads-per-million normalized ChIP-nexus positive strand pooled coverage of Bicoid across 2-3hr Drosophila OreR embryos
• orer_cad_mbt_nexus_combined_normalized_negative.bw: Reads-per-million normalized ChIP-nexus negative strand pooled coverage of Caudal across 2-3hr Drosophila OreR embryos
• orer_cad_mbt_nexus_combined_normalized_positive.bw: Reads-per-million normalized ChIP-nexus positive strand pooled coverage of Caudal across 2-3hr Drosophila OreR embryos
• orer_dl_mbt_nexus_combined_normalized_negative.bw: Reads-per-million normalized ChIP-nexus negative strand pooled coverage of Dorsal across 2-3hr Drosophila OreR embryos
• orer_dl_mbt_nexus_combined_normalized_positive.bw: Reads-per-million normalized ChIP-nexus positive strand pooled coverage of Dorsal across 2-3hr Drosophila OreR embryos
• orer_twi_mbt_nexus_combined_normalized_negative.bw: Reads-per-million normalized ChIP-nexus negative strand pooled coverage of Twist across 2-3hr Drosophila OreR embryos
• orer_twi_mbt_nexus_combined_normalized_positive.bw: Reads-per-million normalized ChIP-nexus positive strand pooled coverage of Twist across 2-3hr Drosophila OreR embryos
• orer_zld_mbt_nexus_combined_normalized_negative.bw: Reads-per-million normalized ChIP-nexus negative strand pooled coverage of Zelda across 2-3hr Drosophila OreR embryos
• orer_zld_mbt_nexus_combined_normalized_positive.bw: Reads-per-million normalized ChIP-nexus positive strand pooled coverage of Zelda across 2-3hr Drosophila OreR embryos
• orer_gaf_mbt_nexus_combined_normalized_negative.bw: Reads-per-million normalized ChIP-nexus negative strand pooled coverage of GAGA-factor across 2-3hr Drosophila OreR embryos
• orer_gaf_mbt_nexus_combined_normalized_positive.bw: Reads-per-million normalized ChIP-nexus positive strand pooled coverage of GAGA-factor across 2-3hr Drosophila OreR embryos
• orer_1to15_atac_combined_cutsites.bw: ATAC-seq pooled cutsite coverage across 1-1.5hr Drosophila OreR embryos
• orer_15to2_atac_combined_cutsites.bw: ATAC-seq pooled cutsite coverage across 1.5-2hr Drosophila OreR embryos
• orer_2to25_atac_combined_cutsites.bw: ATAC-seq pooled cutsite coverage across 2-2.5hr Drosophila OreR embryos
• orer_25to3_atac_combined_cutsites.bw: ATAC-seq pooled cutsite coverage across 2.5-3hr Drosophila OreR embryos