This track collects the cell-type chromatin accessibility tracks from the single-cell ATAC-seq datasets in the UCSC Cell Browser. For each dataset it shows the read-coverage signal (bigWig) and, where the study reported them, the accessible-region peak calls (bigNarrowPeak), split out by cell type. The datasets cover several mouse tissues, including brain, kidney, and choroid plexus.
The subtracks come from these datasets:
This is a faceted collection, so the subtracks are chosen with filter menus rather than a long checkbox list. Use the facets on the track configuration page to narrow the subtracks by dataset, tissue, life stage, condition, data type, assay, and cell type, then turn on the ones you want. Signal subtracks draw as coverage graphs and peak subtracks draw as boxes. Each subtrack links back to its source dataset in the Cell Browser.
All signal subtracks that are turned on share one vertical scale, set from the data in the window being viewed, so tracks drawn at the same position can be compared directly. Because each dataset was normalized by its own pipeline, comparisons are most meaningful between subtracks of the same dataset.
Subtracks are colored by broad cell-type class, so the same class is shown in the same color across datasets (and matches the coloring of the corresponding human track). The classes are:
| Excitatory neuron: glutamatergic neurons of the cortical layers, hippocampal CA fields and dentate gyrus, and claustrum | |
| Inhibitory neuron: GABAergic neurons and interneurons (Pvalb, Sst, Lamp5, and CGE- and MGE-derived types) | |
| Medium spiny neuron: striatal D1 and D2 projection neurons of the direct and indirect pathways | |
| Other neuron: remaining neuronal types, such as Cajal-Retzius cells | |
| Neural progenitor: neuroblasts, radial glia, and other neural progenitors | |
| Astrocyte: central nervous system astroglia, including fibrous and protoplasmic astrocytes, Bergmann glia, and retinal Müller glia | |
| Oligodendrocyte: oligodendrocytes at the newly formed, myelin-forming, and mature stages | |
| Oligodendrocyte precursor: oligodendrocyte precursor cells (OPCs) and committed precursors | |
| Microglia: microglia and perivascular macrophages | |
| Other glia: glia that fit none of the glial classes above, such as olfactory ensheathing cells and clusters labeled only as glia | |
| Ependymal: ependymal cells lining the ventricles | |
| Choroid plexus: choroid plexus epithelial cells | |
| Endothelial: endothelial cells of arteries, capillaries, veins, and endocardium | |
| Mural: pericytes, smooth muscle, and vascular leptomeningeal cells | |
| Immune: lymphoid (B, T) and myeloid (macrophage, dendritic, basophil) immune cells | |
| Erythroid: erythroid cells and erythroblasts | |
| Hematopoietic stem/progenitor: hematopoietic stem and progenitor cells | |
| Cardiomyocyte: heart muscle cells | |
| Muscle: skeletal muscle myofibers, satellite cells, and junctional myonuclei | |
| Epithelial: epithelial cells of many tissues, such as airway, gut, kidney tubule, and secretory epithelia | |
| Stromal: fibroblasts, mesenchymal, and other stromal cells | |
| Other: mixed types, and types that fit none of the classes above, such as peripheral glia (Schwann and enteric) and melanocytes | |
| Unknown: cell type not resolved from the source data |
Each dataset was produced and processed by a different group, so the assays and analysis pipelines vary. The signal and peak files here are the same ones served by the individual Cell Browser datasets, copied into the browser without change. The table summarizes each dataset; see the linked publication for details.
| Dataset | Assay | Processing summary |
|---|---|---|
| CATLAS Mouse Aging Brain | single-cell ATAC-seq | Accessibility profiled across cell types of the aging mouse brain; per-cell-type coverage tracks. |
| CATLAS Adult Mouse Brain | single-cell ATAC-seq | Adult mouse cerebrum nuclei clustered into cell types, with per-cell-type accessibility coverage. |
| Allen Basal Ganglia ATAC | single-nucleus ATAC-seq | Basal ganglia nuclei grouped by region and neuron subtype (e.g. D1/D2 MSNs, dorsal/ventral), coverage per group. |
| Dynamic Responses of Oligodendroglia in EAE Mice | single-cell multiome (ATAC + RNA) | Oligodendroglia profiled across EAE disease progression; the ATAC arm gives per-cell-type accessibility coverage. |
| Mouse Lateral Ventricle Choroid Plexus Multi-omics | single-cell multiome (ATAC + RNA) | Choroid plexus nuclei profiled by multi-omics; ATAC arm gives per-cell-type coverage plus peak calls. |
| CATLAS Adult Mouse Brain Paired-Tag | Paired-Tag (histone + RNA) | Joint histone-modification and transcriptome profiling of adult mouse brain; the accessibility tracks are shown here. |
| Mouse Kidney Regulatory Landscape | single-cell ATAC-seq | Mouse kidney nuclei clustered into cell types; per-cell-type accessibility used to map differentiation programs and disease-relevant regulatory regions. |
| Oligodendrocytes in Mouse EAE Model of MS | single-cell ATAC-seq | Accessibility of the oligodendrocyte lineage in a mouse EAE model of multiple sclerosis. |
| Multimodal Chromatin Profiling of Juvenile Mouse Brain | nanobody-based single-cell CUT&Tag | Multimodal single-cell chromatin profiling of juvenile mouse brain; the accessibility tracks are shown here. |
The steps used to assemble the files into this track are recorded in the makeDoc, which uses the scripts in the singleCellSignalsPeaks directory.
The subtracks can be explored in table form with the Table Browser or the Data Integrator, and read from scripts through our API.
For automated download and analysis, the signal and peak files are stored under http://hgdownload.soe.ucsc.edu/gbdb/mm10/bbi/singleCellSignalsPeaks/, keeping the same per-dataset subdirectories shown on the configuration page. The files can be read with the command-line tools bigWigToBedGraph (for the signal bigWigs) and bigBedToBed (for the peak files), which can be compiled from source or downloaded as precompiled binaries. Both take a region so you do not have to download the whole file, for example:
bigWigToBedGraph -chrom=chr1 -start=3000000 -end=3100000 \
http://hgdownload.soe.ucsc.edu/gbdb/mm10/bbi/singleCellSignalsPeaks/mouse-epi-juv-brain/hub/atac/BG.bw \
stdout
bigBedToBed -chrom=chr19 -start=0 -end=61000000 \
http://hgdownload.soe.ucsc.edu/gbdb/mm10/bbi/singleCellSignalsPeaks/mouse-lvcp-multiome/scMultiome/atac/hub/peaks/all_cells.bb \
stdoutThe underlying matrices, metadata, and per-dataset download details are on each dataset's page in the UCSC Cell Browser.
Thanks to the UCSC Cell Browser team and the research groups whose single-cell datasets are shown here. For questions about a particular subtrack, start with the dataset page it links to.
Bartosovic M, Castelo-Branco G. Multimodal chromatin profiling using nanobody-based single-cell CUT&Tag. Nat Biotechnol. 2023 Jun;41(6):794-805. PMID: 36536148; PMC: PMC10264246
Li YE, Preissl S, Hou X, Zhang Z, Zhang K, Qiu Y, Poirion OB, Li B, Chiou J, Liu H et al. An atlas of gene regulatory elements in adult mouse cerebrum. Nature. 2021 Oct;598(7879):129-136. PMID: 34616068; PMC: PMC8494637
Meijer M, Agirre E, Kabbe M, van Tuijn CA, Heskol A, Zheng C, Mendanha Falcão A, Bartosovic M, Kirby L, Calini D et al. Epigenomic priming of immune genes implicates oligodendroglia in multiple sclerosis susceptibility. Neuron. 2022 Apr 6;110(7):1193-1210.e13. PMID: 35093191; PMC: PMC9810341
Miao Z, Balzer MS, Ma Z, Liu H, Wu J, Shrestha R, Aranyi T, Kwan A, Kondo A, Pontoglio M et al. Single cell regulatory landscape of the mouse kidney highlights cellular differentiation programs and disease targets. Nat Commun. 2021 Apr 15;12(1):2277. PMID: 33859189; PMC: PMC8050063
Zhang Y, Amaral ML, Zhu C, Grieco SF, Hou X, Lin L, Buchanan J, Tong L, Preissl S, Xu X et al. Single-cell epigenome analysis reveals age-associated decay of heterochromatin domains in excitatory neurons in the mouse brain. Cell Res. 2022 Nov;32(11):1008-1021. PMID: 36207411; PMC: PMC9652396
Zheng C, Hervé B, Meijer M, Rubio Rodríguez-Kirby LA, Guerreiro Cacais AO, Kukanja P, Kabbe M, Jimenez-Beristain T, Olsson T, Agirre E et al. Distinct transcriptomic and epigenomic responses of mature oligodendrocytes during disease progression in a mouse model of multiple sclerosis. Nat Neurosci. 2025 Dec;28(12):2612-2627. PMID: 41249698; PMC: PMC12672374
Zhu C, Zhang Y, Li YE, Lucero J, Behrens MM, Ren B. Joint profiling of histone modifications and transcriptome in single cells from mouse brain. Nat Methods. 2021 Mar;18(3):283-292. PMID: 33589836; PMC: PMC7954905