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 and mouse single cell ATAC-seq 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

Mouse adult heart single cell ATAC-seq

mouseadult_heart_atac_matrix.rds (single cell ATAC-seq counts)

mouseadult_heart_cell_annot.txt (cell type annotation for each cell in scATAC-seq matrix)

mouseadult_heart_peak_ids.txt (marker peaks)

1. Pijuan-Sala, B. et al. Single-cell chromatin accessibility maps reveal regulatory programs driving early mouse organogenesis. Nat. Cell Biol. 22, 487–497 (2020).
2. 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).
3. Roadmap Epigenomics Consortium et al. Integrative analysis of 111 reference human epigenomes. Nature 518, 317–330 (2015).
4. Domcke, S. et al. A human cell atlas of fetal chromatin accessibility. Science 370, (2020).
5. Granja, J. M. et al. Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia. Nat. Biotechnol. 37, 1458–1465 (2019).
6. Yang, H. et al. A map of cis-regulatory elements and 3D genome structures in zebrafish. Nature 588, 337–343 (2020).
7. Zabidi, M. A. et al. Enhancer-core-promoter specificity separates developmental and housekeeping gene regulation. Nature 518, 556–559 (2015).