0abed78024d40b506c2b2e3a49ad483045bc5e1d mspeir Sat Aug 1 20:53:25 2026 -0700 singleCellSignalsPeaks: add native mm10 track mm10 counterpart of the hg38 track: 629 single-cell ATAC signal (bigWig) and peak (bigNarrowPeak) subtracks from 9 Cell Browser datasets, re-parented under one faceted composite in the regulation group. Colored by broad cell class from the same palette as hg38, grouped by class, off by default; cell types are paper-curated and the facets/longLabels are harmonized (see the makeDoc). Data lives in /hive/data/genomes/mm10/bed/singleCellSignalsPeaks and is served via the /gbdb/mm10/bbi symlink; the .ra is regenerated by makeSingleCellSignalsPeaksRa.py from the Cell Browser hub build. Included in mm10 trackDb.ra (alpha). refs #37914 Co-Authored-By: Claude Opus 4.8 (1M context) diff --git src/hg/makeDb/trackDb/mouse/mm10/singleCellSignalsPeaks.html src/hg/makeDb/trackDb/mouse/mm10/singleCellSignalsPeaks.html new file mode 100644 index 00000000000..0ebde372f3c --- /dev/null +++ src/hg/makeDb/trackDb/mouse/mm10/singleCellSignalsPeaks.html @@ -0,0 +1,318 @@ +

Description

+

+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: +

+ + +

Display Conventions and Configuration

+

+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. +

+ +

+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 nephron progenitors
 Astrocyte — astrocytes, including Bergmann glia and fibrous and protoplasmic subtypes
 Oligodendrocyte — oligodendrocytes across the newly-formed, myelin-forming, and mature stages
 Oligodendrocyte precursor — oligodendrocyte precursor cells (OPCs) and committed precursors
 Microglia — microglia and perivascular macrophages
 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 — other or mixed cell types, such as olfactory ensheathing cells and melanocytes
 Unknown — cell type not resolved from the source data
+ +

Methods

+

+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 full detail. +

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DatasetAssayProcessing summary
CATLAS Mouse Aging Brainsingle-cell ATAC-seqAccessibility profiled across cell types of the aging mouse brain; per-cell-type coverage tracks.
CATLAS Adult Mouse Brainsingle-cell ATAC-seqAdult mouse cerebrum nuclei clustered into cell types, with per-cell-type accessibility coverage.
Allen Basal Ganglia ATACsingle-nucleus ATAC-seqBasal ganglia nuclei grouped by region and neuron subtype (e.g. D1/D2 MSNs, dorsal/ventral), coverage per group.
Dynamic Responses of Oligodendroglia in EAE Micesingle-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-omicssingle-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-TagPaired-Tag (histone + RNA)Joint histone-modification and transcriptome profiling of adult mouse brain; the accessibility tracks are shown here.
Mouse Kidney Regulatory Landscapesingle-cell ATAC-seqMouse 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 MSsingle-cell ATAC-seqAccessibility of the oligodendrocyte lineage in a mouse EAE model of multiple sclerosis.
Multimodal Chromatin Profiling of Juvenile Mouse Brainnanobody-based single-cell CUT&TagMultimodal 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. +

+ +

Data Access

+

+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 \
+  stdout
+

+The underlying matrices, metadata, and per-dataset download details are on each +dataset's page in the UCSC Cell +Browser. +

+ +

Credits

+

+Thanks to the UCSC Cell Browser team and the research groups whose single-cell +datasets are shown here. Questions about a particular subtrack are best directed +to the dataset page it links to. +

+ +

References

+ + + +

+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 +

+ + + + +

+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 +

+ + + + +

+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 +

+ + + + +

+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 +

+ + + + +

+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 +

+ + + + +

+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 +

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