A Bag-Of-Motif Model Captures Cell States at Distal Regulatory Sequences

The BOM distal cis-regulatory elements (CREs) datasets

This is the set of distal CRE data used in the Bag-Of-Motif paper. Datasets from the references below were processed as described in the BOM paper. Code for the BOM model is found here (https://github.com/ewonglab/BOM_package).

Mouse E8.25 scATAC-seq (Pijuan-Sala, B. et al.)
mouseE8.25_scATAC_cellTypeSpecific_Pijuan_Sala.B_etal_mm10.bed
mouseE8.25_scATAC_cellTypeSpecific_Pijuan_Sala.B_etal_mm10.fa

mouseE8.25_scATAC_topics_Pijuan_Sala.B_etal_mm10.bed
mouseE8.25_scATAC_topics_Pijuan_Sala.B_etal_mm10.fa

Mouse E8.5 etc (Argelaguet, R. et al.)
mouseE8.5_scATAC_cellTypeSpecific_Argelaguet.R_etal_mm10.bed
mouseE8.5_scATAC_cellTypeSpecific_Argelaguet.R_etal_mm10.fa

Human cell lines (Roadmap Epigenomics Consortium et al.)
humanCellLineSpecific_chromHMM_hg19.bed
humanCellLineSpecific_chromHMM_hg19.fa

Human fetal (Domcke, S. et al.)
humanFetal_scATAC_cellTypeSpecific_Domcke.S_etal_hg19.bed    
humanFetal_scATAC_cellTypeSpecific_Domcke.S_etal_hg19.fa

Human blood and bone marrow (Granja, J. M. et al.)
humanHematopoiesis_scATAC_cellTypeSpecific_Granja_J.M_etal_hg19.bed
humanHematopoiesis_scATAC_cellTypeSpecific_Granja_J.M_etal_hg19.fa

Adult zebrafish (Yang, H. et al.)
zebrafishAdult_ATAC_cellTypeSpecific_Yang_H_etal_danRer10.bed
zebrafishAdult_ATAC_cellTypeSpecific_Yang_H_etal_danRer10.fa

Fruit fly (Zabidi, M. A. et al.)
flySTARRseq_dev_hkp_activity_Zabidi_M.A_etal_dm3.bed
flySTARRseq_dev_hkp_activity_Zabidi_M.A_etal_dm3.fa

Pijuan-Sala, B. et al. Single-cell chromatin accessibility maps reveal regulatory programs driving early mouse organogenesis. Nat. Cell Biol. 22, 487–497 (2020).
Argelaguet, R. et al. Decoding gene regulation in the mouse embryo using single-cell multi-omics. 2022.06.15.496239 Preprint at https://doi.org/10.1101/2022.06.15.496239 (2022).
Roadmap Epigenomics Consortium et al. Integrative analysis of 111 reference human epigenomes. Nature 518, 317–330 (2015).
Domcke, S. et al. A human cell atlas of fetal chromatin accessibility. Science 370, (2020).
Granja, J. M. et al. Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia. Nat. Biotechnol. 37, 1458–1465 (2019).
Yang, H. et al. A map of cis-regulatory elements and 3D genome structures in zebrafish. Nature 588, 337–343 (2020).
Zabidi, M. A. et al. Enhancer-core-promoter specificity separates developmental and housekeeping gene regulation. Nature 518, 556–559 (2015).