b914d581f876d486caf9404e715e4f61ada38195 mspeir Mon Aug 3 16:19:44 2026 -0700 singleCellSignalsPeaks: make every subtrack label unique, fix cell-class regressions The harmonized labels were not distinguishing tracks. build_long_label composed from cell type + condition + tissue, but the upstream steps discard the discriminators on purpose to keep the facets compact, so hg38 had 925 subtracks sharing only 401 distinct longLabels and mm10 629 sharing 359. Worst case: cortex-atac's MACS, enhancer and cell-type-specific peak sets all read "Astrocytes and oligodendrocytes (Cortex ATAC)", with the peak method surviving only in the raw shortLabel. Labels are now built from the harmonized cell type plus a variant descriptor that recovers what was dropped (peak method, grouping level, cohort, signal vs peaks), and anything still colliding is qualified with its source cluster code. shortLabels are rebuilt too -- the old ones were raw source strings up to 50 chars with underscores, ArchR filename tails and R-mangled names -- abbreviated through a curated word table to 22 chars, with compact tokens where the longLabel distinction would otherwise be invisible (SEA-AD region + ADNC, CATLAS aging age). All 925/587 longLabels are now unique; no shortLabel exceeds 22 chars or contains an underscore. Also fixed, found while verifying the above: - Correcting source misspellings in the cell types broke the curated lookups, which are keyed on those same misspelled strings, and 16 hg38 tracks silently lost their Cell_class and color. The class map and the hub_config tables now normalize their keys on load, and a cell type with no broad class is reported instead of becoming "unknown". - Nephron progenitor was classed as Neural progenitor: the decode tables give it the bare broad class "Progenitor" and that was blanket-mapped to neural. It is Six2+ kidney cap mesenchyme, so it is now Stromal. The HTML legend had been worded to match the bug. - The plural/case merge picked the most frequent form, which was inconsistent -- singular for 15 of 17 merged groups but plural for Megakaryocytes/Oligodendrocytes. It now prefers the singular. - Removed 42 byte-identical Allen basal-ganglia bigWigs (md5-verified) that were served from four grouping directories and rendered as four indistinguishable mm10 subtracks, freeing 4.4 GB. Where the four copies genuinely differ all are kept and told apart by the grouping-level descriptor. mm10 goes 629 -> 587 subtracks. - Corrected five stale per-dataset subtrack counts in the description pages and spelled out what ADNC means, noting that it grades neuropathology rather than symptoms. - The SEA-AD Dataset facet link used the collection name, which is not a served Cell Browser slug; it now points at sea-ad-mtg+cohort. - Dropped a dead placeholder variable and made the hardcoded hub-build path overridable. refs #37914 Co-Authored-By: Claude Opus 5 (1M context) diff --git src/hg/makeDb/trackDb/mouse/mm10/singleCellSignalsPeaks.html src/hg/makeDb/trackDb/mouse/mm10/singleCellSignalsPeaks.html index 0ebde372f3c..52aaa0e673b 100644 --- src/hg/makeDb/trackDb/mouse/mm10/singleCellSignalsPeaks.html +++ src/hg/makeDb/trackDb/mouse/mm10/singleCellSignalsPeaks.html @@ -1,318 +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
Neural progenitor — neuroblasts, radial glia, and other neural 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.

DatasetAssayProcessing 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.

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