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The genomic coordinates of human cCREs (bed format) predicted by NvwaCE for each cell type.
human_cCREs_predictedBy_NvwaCE-Acinar_cell.bed
human_cCREs_predictedBy_NvwaCE-Adipocyte.bed
human_cCREs_predictedBy_NvwaCE-Adrenal_cortex.bed
human_cCREs_predictedBy_NvwaCE-Alveolar_macrophage.bed
human_cCREs_predictedBy_NvwaCE-Astrocyte.bed
human_cCREs_predictedBy_NvwaCE-Basal-like.bed
human_cCREs_predictedBy_NvwaCE-B_cell.bed
human_cCREs_predictedBy_NvwaCE-Bladder_fibroblast.bed
human_cCREs_predictedBy_NvwaCE-Cardiac_muscle.bed
human_cCREs_predictedBy_NvwaCE-Chief_cell.bed
human_cCREs_predictedBy_NvwaCE-Chromaffin_cell.bed
human_cCREs_predictedBy_NvwaCE-Corticotrope.bed
human_cCREs_predictedBy_NvwaCE-DC.bed
human_cCREs_predictedBy_NvwaCE-Distal_tubule_and_collecting_duct.bed
human_cCREs_predictedBy_NvwaCE-Endocrine_cell.bed
human_cCREs_predictedBy_NvwaCE-Endothelium_Hand2.bed
human_cCREs_predictedBy_NvwaCE-Endothelium_Heyl.bed
human_cCREs_predictedBy_NvwaCE-Endothelium_Ramp3.bed
human_cCREs_predictedBy_NvwaCE-Enterocyte_Large_intestine.bed
human_cCREs_predictedBy_NvwaCE-Enterocyte_Small_intestine.bed
human_cCREs_predictedBy_NvwaCE-Erythroid.bed
human_cCREs_predictedBy_NvwaCE-Fibroblast_Fmo3.bed
human_cCREs_predictedBy_NvwaCE-Foveolar_cell.bed
human_cCREs_predictedBy_NvwaCE-GABAergic_Dlx1.bed
human_cCREs_predictedBy_NvwaCE-Gastrointestinal_fibroblast.bed
human_cCREs_predictedBy_NvwaCE-Goblet_cell.bed
human_cCREs_predictedBy_NvwaCE-Gonadotrope.bed
human_cCREs_predictedBy_NvwaCE-Granule_cell.bed
human_cCREs_predictedBy_NvwaCE-Granulosa_cell.bed
human_cCREs_predictedBy_NvwaCE-Hepatic_stellate_cell.bed
human_cCREs_predictedBy_NvwaCE-Hepatocyte.bed
human_cCREs_predictedBy_NvwaCE-Immature_B.bed
human_cCREs_predictedBy_NvwaCE-Lactotrope.bed
human_cCREs_predictedBy_NvwaCE-Liver_sinusoidal_endothelium.bed
human_cCREs_predictedBy_NvwaCE-Lymphatic_endothelium.bed
human_cCREs_predictedBy_NvwaCE-Macrophage.bed
human_cCREs_predictedBy_NvwaCE-Medium_spiny_neuron.bed
human_cCREs_predictedBy_NvwaCE-Meningeal_cell.bed
human_cCREs_predictedBy_NvwaCE-Mesothelial_cell.bed
human_cCREs_predictedBy_NvwaCE-Microglia.bed
human_cCREs_predictedBy_NvwaCE-Mucous_neck_cell.bed
human_cCREs_predictedBy_NvwaCE-Muscular_endothelium.bed
human_cCREs_predictedBy_NvwaCE-Muscular_fibroblast.bed
human_cCREs_predictedBy_NvwaCE-Neural_endothelium.bed
human_cCREs_predictedBy_NvwaCE-Neuron_Lin28b.bed
human_cCREs_predictedBy_NvwaCE-Neuron_Satb2.bed
human_cCREs_predictedBy_NvwaCE-Neutrophil.bed
human_cCREs_predictedBy_NvwaCE-NK.bed
human_cCREs_predictedBy_NvwaCE-Oligodendrocyte.bed
human_cCREs_predictedBy_NvwaCE-Oligodendrocyte_progenitor_cell.bed
human_cCREs_predictedBy_NvwaCE-Pancreatic_secretory_cell.bed
human_cCREs_predictedBy_NvwaCE-Paneth_cell.bed
human_cCREs_predictedBy_NvwaCE-Parietal_cell.bed
human_cCREs_predictedBy_NvwaCE-pDC.bed
human_cCREs_predictedBy_NvwaCE-Pericyte.bed
human_cCREs_predictedBy_NvwaCE-Pituitary_stem_cell.bed
human_cCREs_predictedBy_NvwaCE-Plasma_cell.bed
human_cCREs_predictedBy_NvwaCE-Proximal_tubule_1.bed
human_cCREs_predictedBy_NvwaCE-Proximal_tubule_2.bed
human_cCREs_predictedBy_NvwaCE-Pulmonary_endotehlium.bed
human_cCREs_predictedBy_NvwaCE-Pulmonary_epithelium.bed
human_cCREs_predictedBy_NvwaCE-Reproductive_fibroblast.bed
human_cCREs_predictedBy_NvwaCE-Schwann_cell.bed
human_cCREs_predictedBy_NvwaCE-Skeletal_muscle.bed
human_cCREs_predictedBy_NvwaCE-Smooth_muscle_cell.bed
human_cCREs_predictedBy_NvwaCE-Somatotrope.bed
human_cCREs_predictedBy_NvwaCE-T_cell.bed
human_cCREs_predictedBy_NvwaCE-Thymocyte.bed
human_cCREs_predictedBy_NvwaCE-Thyrotrope.bed
human_cCREs_predictedBy_NvwaCE-Urothelial_cell.bed
human_cCREs_predictedBy_NvwaCE-Uterine_epithelium.bed

The genomic coordinates of cCREs (bed format) predicted by NvwaCE across five mammals.
monkey_cCREs_predictedBy_NvwaCE.bed
cow_cCREs_predictedBy_NvwaCE.bed
horse_cCREs_predictedBy_NvwaCE.bed
panda_cCREs_predictedBy_NvwaCE.bed
pig_cCREs_predictedBy_NvwaCE.bed
sheep_cCREs_predictedBy_NvwaCE.bed

Normalized fragment pileup profiles (bigwig format) for each subcluster.
Mouse (Male)
Endothelium_Hoxb9
Liver_sinusoidal_endothelium
Lung_endothelium
Lymphatic_endothelium
Muscular_endothelium
nephritic_endothelium
Neural_endothelium
Pericyte
splenic_endothelium
Acinar_cell
AT1
AT2
Basal_cell
Bladder_basal_cell
Chief_cell
Club_cell
Collecting_duct
Distal_tubule
Enterocyte
Epididymis_epithelial_cell
Foveolar_cell
Luminal_cell
nephron_progenitor
Paneth_cell
Parietal_cell
Proximal_tubule
Seminal_vesicle_epithelial_cell
Thymic_epithelial_cell
Urothelial_cell
Erythroid_cell
Hepatocyte
Alveolar_macrophage
B_cell
Dendritic_cell
Macrophage
Monocyte
Neutrophil
NK
Plasma_cell
T_cell
Thymocyte
Cardiac_muscle
Skeletal_muscle
Smooth_muscle_cell
Astrocyte
Cerebellar_GABAergic
Corticotrope/Gonadotrope
GABAergic_Dlx1
Glutamatergic_Glis3
Glutamatergic_Satb2
Granule_cell
Lactotrope
Medium_spiny_neuron
Neuron_Lin28b
Oligodendrocyte
Oligodendrocyte_progenitor
Pituitary_stem_cell
Schwann_cell
Somatotropes
Leydig_cell
Sertoli_cell
Spermatocyte
Endocrine_cell
Pancreatic_secretory_cell
Adipocyte
Airway_goblet_cell
Bladder_fibroblast
Fibroblast
Hepatic_stellate_cell
Immune_fibroblast
Lung_fibroblast
Meningeal_cell
Mesangial_cell
Mesothelial_cell
Myoepithelial_cell
Podocyte
Satellite_cell
Mouse (Female)
Endothelium_Hand2
Endothelium_Heyl
Endothelium_Ramp3
Liver_sinusoidal_endothelium
Lymphatic_endothelium
Muscular_endothelium
Neural_endothelium
Pulmonary_endotehlium
Acinar_cell
Basal-like
Chief_cell
Distal_tubule_and_collecting_duct
Enterocyte_Large_intestine
Enterocyte_Small_intestine
Foveolar_cell
Goblet_cell
Mucous_neck_cell
Paneth_cell
Parietal_cell
Proximal_tubule_1
Proximal_tubule_2
Pulmonary_epithelium
Urothelial_cell
Uterine_epithelium
Erythroid
Hepatocyte
Alveolar_macrophage
B_cell
DC
Immature_B
Macrophage
Microglia
Neutrophil
NK
pDC
Plasma_cell
T_cell
Thymocyte
Cardiac_muscle
Skeletal_muscle
Smooth_muscle_cell
Astrocyte
Chromaffin_cell
Corticotrope
GABAergic_Dlx1
Gonadotrope
Granule_cell
Lactotrope
Medium_spiny_neuron
Neuron_Lin28b
Neuron_Satb2
Oligodendrocyte
Oligodendrocyte_progenitor_cell
Pituitary_stem_cell
Schwann_cell
Somatotrope
Thyrotrope
Granulosa_cell
Adrenal_cortex
Endocrine_cell
Pancreatic_secretory_cell
Adipocyte
Bladder_fibroblast
Fibroblast_Fmo3
Gastrointestinal_fibroblast
Hepatic_stellate_cell
Meningeal_cell
Mesothelial_cell
Muscular_fibroblast
Pericyte
Reproductive_fibroblast
Chicken
Cerebral_endothelium
Endothelium_ENTPD1
Endothelium_GPR68
Endothelium_MEOX2
Endothelium_PDGFRB
Endothelium_SELE
Kidney_endothelium
Liver_endothelium
Liver_sinusoidal_endothelium
Lung_endothelium
Lymphatic_endothelium
Neural_endothelium
Acinar_cell
Airsac_epithelium
Cloacal_epithelium_1
Cloacal_epithelium_2
Distal_tubule_and_collecting_duct
Enterocyte_Cecum/Bowel
Enterocyte_Duodenum/Ileum
Foveolar_cell
Goblet_cell
Parietal_cell
Proximal_tubule
Pulmonary_epithelium
Erythroid
Hepatocyte
B_cell
Megakaryocyte
Monocyte
Myeloid_cell
Plasma_cell_1
Plasma_cell_2
T_cell
Myocyte
Smooth_muscle_cell
Astrocyte
Bergmann_glia
Cerebral_astocyte
Cerebral_oligodendrocyte_progenitor
GABAergic_neuron
Granule_cell
Neuroendocrine_cell
Oligodendrocyte
Oligodendrocyte_progenitor
Pancreatic_secretory_cell
Epicardium
Fibroblast_BARX1
Fibroblast_CDH5
Fibroblast_COL1A2
Fibroblast_COL9A1
Fibroblast_CXCL14
Fibroblast_MMP9
Immune-like
Myofibroblast
Gecko
Endocardium
Endothelium_ADGRG1
Endothelium_CLDN11
Fat_body_endothelium
Liver_sinusoidal_endothelium
Lung_endothelium
Lymphatic_endothelium
Renal_endothelium
Acinar_cell
Basal_cell
Cloacal_epithelium
Collecting_duct_
Distal_tubule
Enterocyte
Foveolar_cell
Goblet_cell
Mucous_neck_cell
Parietal_cell
Proximal_tubule
Pulmonary_epithelium
Skin_keratinocyte
Tongue_keratinocyte
Urothelial_cell
Cycling_erythroid_cell
Erythroid_cell
Hepatocyte
B_cell
Macrophage
Megakaryocyte
Neutrophil
Plasma_cell
T_cell
Cardiac_muscle
Skeletal_muscle
Bipolar_cell
Cerebral_astrocyte
Cerebral_neuron
Lens_epithelial_cell
Oligodendrocyte
Photoreceptor_cell
Retinal_astrocyte
Retinal_ganglion_cell
Retinal_pigment_epithelium
Cumulus_cell
Mural_granulosa_cell
Endocrine_cell
Pancreatic_secretory_cell
Adipocyte
Chondrocyte
Epicardium
Fibroblast
Lung_fibroblast
Mesothelial_cell
Smooth_muscle_cell
Axolotl
Capillary_endothelial_cell
Endocardial_endothelial_cell
Endothelial_MAS1
Endothelial_RGS5
Liver_sinusoidal_endothelial_cell
Lymphatic_endothelial_cell
Acinar_cell
Basal_cell
Cholangiocyte
Cloaca_epithelial_cell
Enterocyte
Foveolar_cell
Goblet_cell
H+_secreting_cell
Pancreatic_ductal_cell
Parietal_cell
Proximal_tubule
Pulmonary_epithelium
Respiratory_epithelial_cell
Urothelial_cell
vas_deferens_epithelial_cell
Erythroid_cell
Hepatocyte
B_cell
Macrophage
Megakaryocyte
T_cell
Cardiac_muscle
Smooth_muscle_cell
Astrocyte
Inhibitory_neuron
Neuroendocrine
Neuron_NR4A1
Neuron_UNC5A
Oligodendrocyte
Oligodendrocyte_progenitor
Endocrine_cell
Adipocyte
Chondrocyte
Epicardial_cell
Fibroblast
Fibroblast_GPRC6A
Hepatic_stellate_cell
Lung_fibroblast
Meningeal_cell
Mesothelial_cell
Myoblast
Myofibroblast
Osteoblast
Podocyte
Zebrafish
Endocardium
Endothelium_meox2a
Erythroid-like_endothelium
Liver_sinusoidal_endothelium
Lymphatic_endothelium
Neural_endothelium
Swim_bladder_endothelium
Caudal_fin_epithelium
Cholangiocyte
Ciliated_cell
Gill_epithelial_1
Gill_epithelial_2
Goblet_cell
Intestinal_and_pancreatic
Ionocyte
Swim_bladder_epithelium
Erythroid
Hepatocyte
B_cell
Megakaryocyte
Myeloid
NK
T_cell
Cardiac_muscle
Skeletal_muscle
Smooth_muscle_cell
vSMC
Astrocyte
Granule_cell
Meningeal_cell
Neuron
Oligodendrocyte
Corpus_luteum
Germ_cell
Granulosa_cell
Leydig/Theca
mmp11b+
Ovarian_epithelium
Sertoli_cell
Adipocyte
Chondrocyte
Epicardium
Fibroblast_osr1
Fibroblast_podxl
Myofibroblast
Ovary_fibroblast_1
Ovary_fibroblast_2
Pericyte
Pharyngeal_arch
Swim_bladder_fibroblast
Xanthoblast

Unprocessed bam files, demultiplexed fragment files, metadata, processed data and custom code and scripts.

Raw Data: GSE284189 (token: onyxsskcfnsrlat)

Unprocessed bam files, demultiplexed fragment files and metadata are available in the NCBI Gene Expression Omnibus (GEO) under accession number GSE284189.

Analyzed/Processed Data: https://figshare.com/s/0dfc0ba97f54b429af69

Custom code and scripts: https://github.com/ehcilc23/UUATAC

The pre-trained NvwaCE model: https://github.com/ehcilc23/UUATAC