38d5c1e91f3a867c589da441f549c9d46bc9b9f4 mspeir Mon Jul 20 14:05:31 2026 -0700 Add singleCellSignalsPeaks track to hg38 Native faceted composite built from the per-cell-type signal (bigWig) and peak (bigBed/bigNarrowPeak) tracks of the UCSC Cell Browser single-cell ATAC datasets, re-parented under one track in the regulation group. 936 subtracks across 9 datasets. Data files live in /hive/data/genomes/hg38/bed/singleCellSignalsPeaks and are served via a /gbdb/hg38/bbi symlink; the .ra is regenerated from the Cell Browser hub build by makeDb/scripts/singleCellSignalsPeaks/makeSingleCellSignalsPeaksRa.py. refs #37820 Co-Authored-By: Claude Opus 4.8 (1M context) diff --git src/hg/makeDb/trackDb/human/hg38/singleCellSignalsPeaks.html src/hg/makeDb/trackDb/human/hg38/singleCellSignalsPeaks.html new file mode 100644 index 00000000000..f7150229478 --- /dev/null +++ src/hg/makeDb/trackDb/human/hg38/singleCellSignalsPeaks.html @@ -0,0 +1,266 @@ +

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 (bigBed and narrowPeak), split +out by cell type. The datasets cover several human tissues, including brain, +heart, and retina. +

+The subtracks come from these datasets: +

+ Human Enhancer Atlas: + chromatin accessibility across 30 adult and 15 fetal human tissue types, + describing about 1.2 million candidate cis-regulatory elements in 222 cell + types. 222 signal and 222 peak subtracks (Zhang et al. 2021). +
+ Cortex ATAC: + single-cell epigenomes of the developing human brain and cortical + organoids. 12 signal and 79 peak subtracks (Ziffra et al. 2021). +
+ Human and Mouse Retina Cell Atlas: + accessibility across retinal cell types. 39 signal and 30 peak subtracks + (Li et al. 2023, preprint). +
+ Risk Loci in Alzheimer's and Parkinson's: + accessibility of six adult human brain regions, defining 359,022 cell + type-specific regulatory elements used to interpret disease-associated + variants. 65 signal and 2 peak subtracks (Corces et al. 2020). +
+ Multiomic Human Heart: + accessibility across human cardiac development, aging, and disease, paired + with expression data. 40 signal subtracks (Gao et al. 2026). +
+ Human Cardiogenesis: + accessibility of human fetal hearts at three early developmental stages, + used to prioritize noncoding variants in congenital heart disease. 19 + signal subtracks (Ameen et al. 2022). +
+ Oligodendrocytes in Mouse EAE Model of MS: + accessibility in the oligodendrocyte lineage; the tracks here are the + accessibility measured in oligodendroglia from adult human brain. 18 signal + subtracks (Meijer et al. 2022). +
+ BrainVar: + gene-activity signal from snATAC-seq of prenatal dorsolateral prefrontal + cortex. 4 signal subtracks. +
+ SEA-AD Brain ATAC: + chromatin accessibility per cell subclass across the spectrum of Alzheimer's + disease neuropathological change, from middle temporal gyrus and prefrontal + cortex; tracks are colored by SEA-AD subclass. 184 signal subtracks + (Gabitto et al. 2024). +

+ +

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. +

+ +

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. +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Dataset	Assay	Processing summary
Human Enhancer Atlas	single-cell ATAC-seq (adult and fetal tissues)	Accessibility profiled across 30 adult and 15 fetal tissues, integrated to call about 1.2 million candidate cis-regulatory elements across 222 cell types.
Cortex ATAC	10x single-cell ATAC-seq	Developing human cortex and organoid nuclei clustered by accessibility; gene-activity signal derived from accessibility near genes.
Human and Mouse Retina Cell Atlas	single-nucleus ATAC-seq	Retinal nuclei clustered into cell types, with per-cell-type coverage and peak calls.
Risk Loci in Alzheimer's and Parkinson's	10x single-cell ATAC-seq	70,631 nuclei from six adult brain regions clustered by iterative LSI; peaks called per cluster with MACS2 (501 bp summits, blacklist-filtered), giving 359,022 cell type-specific elements.
Multiomic Human Heart	single-nucleus ATAC-seq (with snRNA-seq)	106 snATAC datasets processed with SnapATAC2, batch-corrected by donor and study, integrated with expression from 299 donors.
Human Cardiogenesis	single-cell ATAC-seq	Human fetal hearts from three early stages profiled to map dynamic regulatory elements across cardiac differentiation trajectories.
Oligodendrocytes in Mouse EAE Model of MS	single-cell ATAC-seq	Accessibility of the oligodendrocyte lineage; the human tracks show accessibility in oligodendroglia from adult human brain.
BrainVar	single-nucleus ATAC-seq	Prenatal dorsolateral prefrontal cortex nuclei summarized as gene-activity coverage per major cell class.
SEA-AD Brain ATAC	single-nucleus ATAC-seq	Pseudobulk accessibility per cell subclass across donors spanning the full range of Alzheimer's disease neuropathological change, from middle temporal gyrus and prefrontal cortex; tracks colored by SEA-AD subclass.

+The steps used to assemble the files into this track are recorded in the +makeDoc. +

+ +

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/hg38/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=1000000 -end=1100000 \
+  http://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/singleCellSignalsPeaks/neuro-degen-atac/bigWig/neuronal-celltypes/projNeuron_LDSCgroup-VIP_Interneurons_GRanges_insertions_bin100_RIPnorm.bw \
+  stdout
+
+bigBedToBed -chrom=chr21 -start=0 -end=48000000 \
+  http://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/singleCellSignalsPeaks/cortex-atac/hub/Enhancerpeaks/AstroOligo.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 K, Hocker JD, Miller M, Hou X, Chiou J, Poirion OB, Qiu Y, Li YE, Gaulton KJ, Wang A et +al. + +A single-cell atlas of chromatin accessibility in the human genome. +Cell. 2021 Nov 24;184(24):5985-6001.e19. +PMID: 34774128; PMC: PMC8664161 +

+ +

+Ziffra RS, Kim CN, Ross JM, Wilfert A, Turner TN, Haeussler M, Casella AM, Przytycki PF, Keough KC, +Shin D et al. + +Single-cell epigenomics reveals mechanisms of human cortical development. +Nature. 2021 Oct;598(7879):205-213. +PMID: 34616060; PMC: PMC8494642 +

+ +

+Li J, Wang J, Ibarra IL, Cheng X, Luecken MD, Lu J, Monavarfeshani A, Yan W, Zheng Y, Zuo Z et +al. + +Integrated multi-omics single cell atlas of the human retina. +bioRxiv. 2023 Nov 8. +

+ +

+Corces MR, Shcherbina A, Kundu S, Gloudemans MJ, Frésard L, Granja JM, Louie BH, Eulalio T, Shams S, +Bagdatli ST et al. + +Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for +Alzheimer's and Parkinson's diseases. +Nat Genet. 2020 Nov;52(11):1158-1168. +PMID: 33106633; PMC: PMC7606627 +

+ +

+Gao W, Hu P, Wick B, Qiu Q, Zhang H, Li Y, Kang X, Bedi K, Haeussler M, Sasaki K et al. + +An integrative single-nucleus multiomic atlas of the human left ventricle identifies gene regulatory +network dynamics across cardiac development, aging, and disease. +Genome Biol. 2026 Apr 6;27(1). +PMID: 41937210; PMC: PMC13067603 +

+ +

+Ameen M, Sundaram L, Shen M, Banerjee A, Kundu S, Nair S, Shcherbina A, Gu M, Wilson KD, Varadarajan +A et al. + +Integrative single-cell analysis of cardiogenesis identifies developmental trajectories and non- +coding mutations in congenital heart disease. +Cell. 2022 Dec 22;185(26):4937-4953.e23. +PMID: 36563664; PMC: PMC10122433 +

+ +

+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 +

+ +

+Gabitto MI, Travaglini KJ, Rachleff VM, Kaplan ES, Long B, Ariza J, Ding Y, Mahoney JT, Dee N, Goldy +J et al. + +Integrated multimodal cell atlas of Alzheimer's disease. +Nat Neurosci. 2024 Dec;27(12):2366-2383. +PMID: 39402379; PMC: PMC11614693 +

+ +

+Hawrylycz M, Kaplan ES, Travaglini KJ, Gabitto MI, Miller JA, Ng L, Close JL, Hodge RD, Long B, +Mollenkopf T et al. + +SEA-AD is a multimodal cellular atlas and resource for Alzheimer's disease. +Nat Aging. 2024 Oct;4(10):1331-1334. +PMID: 39402332; PMC: PMC11577961 +