A Bag-Of-Motif Model Captures Cell States at Distal Regulatory Sequences
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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) 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).
# BOM远端顺式调控元件（cis-regulatory elements, CREs）数据集 本数据集为《Bag-Of-Motif》（简称BOM）论文中使用的远端顺式调控元件与小鼠单细胞ATAC-seq数据集。下述参考文献中的数据集均按照BOM论文中的标准流程进行预处理。BOM模型的代码可于https://github.com/ewonglab/BOM_package 获取。 小鼠E8.25时期单细胞ATAC-seq（Pijuan-Sala, B. 等） 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 小鼠E8.5时期及相关数据集（Argelaguet, R. 等） mouseE8.5_scATAC_cellTypeSpecific_Argelaguet.R_etal_mm10.bed mouseE8.5_scATAC_cellTypeSpecific_Argelaguet.R_etal_mm10.fa 人类细胞系数据集（Roadmap表观基因组联盟等） humanCellLineSpecific_chromHMM_hg19.bed humanCellLineSpecific_chromHMM_hg19.fa 人类胎儿组织数据集（Domcke, S. 等） humanFetal_scATAC_cellTypeSpecific_Domcke.S_etal_hg19.bed humanFetal_scATAC_cellTypeSpecific_Domcke.S_etal_hg19.fa 人类血液与骨髓数据集（Granja, J. M. 等） humanHematopoiesis_scATAC_cellTypeSpecific_Granja_J.M_etal_hg19.bed humanHematopoiesis_scATAC_cellTypeSpecific_Granja_J.M_etal_hg19.fa 成年斑马鱼数据集（Yang, H. 等） zebrafishAdult_ATAC_cellTypeSpecific_Yang_H_etal_danRer10.bed zebrafishAdult_ATAC_cellTypeSpecific_Yang_H_etal_danRer10.fa 果蝇数据集（Zabidi, M. A. 等） flySTARRseq_dev_hkp_activity_Zabidi_M.A_etal_dm3.bed flySTARRseq_dev_hkp_activity_Zabidi_M.A_etal_dm3.fa 小鼠成年心脏单细胞ATAC-seq数据集 mouseadult_heart_atac_matrix.rds（单细胞ATAC-seq计数矩阵） mouseadult_heart_cell_annot.txt（scATAC-seq矩阵中各细胞的细胞类型注释文件） mouseadult_heart_peak_ids.txt（标记峰文件） Pijuan-Sala, B. 等. 单细胞染色质可及性图谱揭示驱动小鼠早期器官发生的调控程序. 自然·细胞生物学, 22, 487–497 (2020). Argelaguet, R. 等. 利用单细胞多组学解码小鼠胚胎中的基因调控. 预印本: https://doi.org/10.1101/2022.06.15.496239 (2022). Roadmap Epigenomics Consortium 等. 111个人类参考表观基因组的整合分析. 自然, 518, 317–330 (2015). Domcke, S. 等. 人类胎儿染色质可及性细胞图谱. 科学, 370, (2020). Granja, J. M. 等. 单细胞多组学分析识别混合表型急性白血病中的调控程序. 自然·生物技术, 37, 1458–1465 (2019). Yang, H. 等. 斑马鱼顺式调控元件与三维基因组结构图谱. 自然, 588, 337–343 (2020). Zabidi, M. A. 等. 增强子-核心启动子特异性区分发育基因与持家基因的调控. 自然, 518, 556–559 (2015).
