037672a61d01d3109e8b20dff4d9142f3c8a8c66
mspeir
Mon Jul 20 16:28:24 2026 -0700
singleCellSignalsPeaks.html: reword two dataset descriptions
Recast two dangling participial phrases ("...describing about 1.2 million
elements", "...defining 359,022 elements") as plain clauses.
refs #37820
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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<h2>Description</h2>
<p>
This track collects the cell-type chromatin accessibility tracks from the
single-cell ATAC-seq datasets in the
<a href="https://cells.ucsc.edu" target="_blank">UCSC Cell Browser</a>. 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.
</p>
<p>
The subtracks come from these datasets:
</p>
<ul>
<li>
<b><a href="https://cells.ucsc.edu/?ds=human-enhancer-atlas" target="_blank">Human Enhancer Atlas</a></b>:
- 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).
+ chromatin accessibility across 30 adult and 15 fetal human tissue types;
+ the study mapped about 1.2 million candidate cis-regulatory elements across
+ 222 cell types. 222 signal and 222 peak subtracks (Zhang et al. 2021).
</li>
<li>
<b><a href="https://cells.ucsc.edu/?ds=cortex-atac" target="_blank">Cortex ATAC</a></b>:
single-cell epigenomes of the developing human brain and cortical
organoids. 12 signal and 79 peak subtracks (Ziffra et al. 2021).
</li>
<li>
<b><a href="https://cells.ucsc.edu/?ds=retina" target="_blank">Human and Mouse Retina Cell Atlas</a></b>:
accessibility across retinal cell types. 39 signal and 30 peak subtracks
(Li et al. 2023, preprint).
</li>
<li>
<b><a href="https://cells.ucsc.edu/?ds=neuro-degen-atac" target="_blank">Risk Loci in Alzheimer's and Parkinson's</a></b>:
- accessibility of six adult human brain regions, defining 359,022 cell
+ accessibility across six adult human brain regions, with 359,022 cell
type-specific regulatory elements used to interpret disease-associated
variants. 65 signal and 2 peak subtracks (Corces et al. 2020).
</li>
<li>
<b><a href="https://cells.ucsc.edu/?ds=multiomic-human-heart" target="_blank">Multiomic Human Heart</a></b>:
accessibility across human cardiac development, aging, and disease, paired
with expression data. 40 signal subtracks (Gao et al. 2026).
</li>
<li>
<b><a href="https://cells.ucsc.edu/?ds=cardiogenesis-atac" target="_blank">Human Cardiogenesis</a></b>:
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).
</li>
<li>
<b><a href="https://cells.ucsc.edu/?ds=olg-eae-ms" target="_blank">Oligodendrocytes in Mouse EAE Model of MS</a></b>:
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).
</li>
<li>
<b><a href="https://cells.ucsc.edu/?ds=brainvar+gene-activity" target="_blank">BrainVar</a></b>:
gene-activity signal from snATAC-seq of prenatal dorsolateral prefrontal
cortex. 4 signal subtracks.
</li>
<li>
<b><a href="https://cells.ucsc.edu/?ds=sea-ad-mtg+cohort" target="_blank">SEA-AD Brain ATAC</a></b>:
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).
</li>
</ul>
<h2>Display Conventions and Configuration</h2>
<p>
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.
</p>
<h2>Methods</h2>
<p>
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.
</p>
<table class="stdTbl">
<tr><th>Dataset</th><th>Assay</th><th>Processing summary</th></tr>
<tr>
<td>Human Enhancer Atlas</td>
<td>single-cell ATAC-seq (adult and fetal tissues)</td>
<td>Accessibility profiled across 30 adult and 15 fetal tissues, integrated to call about 1.2 million candidate cis-regulatory elements across 222 cell types.</td>
</tr>
<tr>
<td>Cortex ATAC</td>
<td>10x single-cell ATAC-seq</td>
<td>Developing human cortex and organoid nuclei clustered by accessibility; gene-activity signal derived from accessibility near genes.</td>
</tr>
<tr>
<td>Human and Mouse Retina Cell Atlas</td>
<td>single-nucleus ATAC-seq</td>
<td>Retinal nuclei clustered into cell types, with per-cell-type coverage and peak calls.</td>
</tr>
<tr>
<td>Risk Loci in Alzheimer's and Parkinson's</td>
<td>10x single-cell ATAC-seq</td>
<td>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.</td>
</tr>
<tr>
<td>Multiomic Human Heart</td>
<td>single-nucleus ATAC-seq (with snRNA-seq)</td>
<td>106 snATAC datasets processed with SnapATAC2, batch-corrected by donor and study, integrated with expression from 299 donors.</td>
</tr>
<tr>
<td>Human Cardiogenesis</td>
<td>single-cell ATAC-seq</td>
<td>Human fetal hearts from three early stages profiled to map dynamic regulatory elements across cardiac differentiation trajectories.</td>
</tr>
<tr>
<td>Oligodendrocytes in Mouse EAE Model of MS</td>
<td>single-cell ATAC-seq</td>
<td>Accessibility of the oligodendrocyte lineage; the human tracks show accessibility in oligodendroglia from adult human brain.</td>
</tr>
<tr>
<td>BrainVar</td>
<td>single-nucleus ATAC-seq</td>
<td>Prenatal dorsolateral prefrontal cortex nuclei summarized as gene-activity coverage per major cell class.</td>
</tr>
<tr>
<td>SEA-AD Brain ATAC</td>
<td>single-nucleus ATAC-seq</td>
<td>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.</td>
</tr>
</table>
<p>
The steps used to assemble the files into this track are recorded in the
<a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/singleCellSignalsPeaks.txt" target="_blank">makeDoc</a>.
</p>
<h2>Data Access</h2>
<p>
The subtracks can be explored in table form with the
<a href="hgTables">Table Browser</a> or the
<a href="hgIntegrator">Data Integrator</a>, and read from scripts through our
<a href="https://api.genome.ucsc.edu" target="_blank">API</a>.
</p>
<p>
For automated download and analysis, the signal and peak files are stored under
<a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/singleCellSignalsPeaks/" target="_blank">http://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/singleCellSignalsPeaks/</a>,
keeping the same per-dataset subdirectories shown on the configuration page. The
files can be read with the command-line tools <tt>bigWigToBedGraph</tt> (for the
signal bigWigs) and <tt>bigBedToBed</tt> (for the peak files), which can be
compiled from source or downloaded as
<a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads" target="_blank">precompiled binaries</a>.
Both take a region so you do not have to download the whole file, for example:
</p>
<pre><code>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</code></pre>
<p>
The underlying matrices, metadata, and per-dataset download details are on each
dataset's page in the <a href="https://cells.ucsc.edu" target="_blank">UCSC Cell
Browser</a>.
</p>
<h2>Credits</h2>
<p>
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.
</p>
<h2>References</h2>
<p>
Zhang K, Hocker JD, Miller M, Hou X, Chiou J, Poirion OB, Qiu Y, Li YE, Gaulton KJ, Wang A <em>et
al</em>.
<a href="https://linkinghub.elsevier.com/retrieve/pii/S0092-8674(21)01279-4" target="_blank">
A single-cell atlas of chromatin accessibility in the human genome</a>.
<em>Cell</em>. 2021 Nov 24;184(24):5985-6001.e19.
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/34774128" target="_blank">34774128</a>; PMC: <a
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8664161/" target="_blank">PMC8664161</a>
</p>
<p>
Ziffra RS, Kim CN, Ross JM, Wilfert A, Turner TN, Haeussler M, Casella AM, Przytycki PF, Keough KC,
Shin D <em>et al</em>.
<a href="https://doi.org/10.1038/s41586-021-03209-8" target="_blank">
Single-cell epigenomics reveals mechanisms of human cortical development</a>.
<em>Nature</em>. 2021 Oct;598(7879):205-213.
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/34616060" target="_blank">34616060</a>; PMC: <a
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8494642/" target="_blank">PMC8494642</a>
</p>
<p>
Li J, Wang J, Ibarra IL, Cheng X, Luecken MD, Lu J, Monavarfeshani A, Yan W, Zheng Y, Zuo Z <em>et
al</em>.
<a href="https://www.biorxiv.org/content/10.1101/2023.11.07.566105v1" target="_blank">
Integrated multi-omics single cell atlas of the human retina</a>.
<em>bioRxiv</em>. 2023 Nov 8.
</p>
<p>
Corces MR, Shcherbina A, Kundu S, Gloudemans MJ, Frésard L, Granja JM, Louie BH, Eulalio T, Shams S,
Bagdatli ST <em>et al</em>.
<a href="https://doi.org/10.1038/s41588-020-00721-x" target="_blank">
Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for
Alzheimer's and Parkinson's diseases</a>.
<em>Nat Genet</em>. 2020 Nov;52(11):1158-1168.
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/33106633" target="_blank">33106633</a>; PMC: <a
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7606627/" target="_blank">PMC7606627</a>
</p>
<p>
Gao W, Hu P, Wick B, Qiu Q, Zhang H, Li Y, Kang X, Bedi K, Haeussler M, Sasaki K <em>et al</em>.
<a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-026-04061-7" target="_blank">
An integrative single-nucleus multiomic atlas of the human left ventricle identifies gene regulatory
network dynamics across cardiac development, aging, and disease</a>.
<em>Genome Biol</em>. 2026 Apr 6;27(1).
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/41937210" target="_blank">41937210</a>; PMC: <a
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13067603/" target="_blank">PMC13067603</a>
</p>
<p>
Ameen M, Sundaram L, Shen M, Banerjee A, Kundu S, Nair S, Shcherbina A, Gu M, Wilson KD, Varadarajan
A <em>et al</em>.
<a href="https://linkinghub.elsevier.com/retrieve/pii/S0092-8674(22)01503-3" target="_blank">
Integrative single-cell analysis of cardiogenesis identifies developmental trajectories and non-
coding mutations in congenital heart disease</a>.
<em>Cell</em>. 2022 Dec 22;185(26):4937-4953.e23.
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/36563664" target="_blank">36563664</a>; PMC: <a
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10122433/" target="_blank">PMC10122433</a>
</p>
<p>
Meijer M, Agirre E, Kabbe M, van Tuijn CA, Heskol A, Zheng C, Mendanha Falcão A, Bartosovic M, Kirby
L, Calini D <em>et al</em>.
<a href="https://linkinghub.elsevier.com/retrieve/pii/S0896-6273(21)01089-8" target="_blank">
Epigenomic priming of immune genes implicates oligodendroglia in multiple sclerosis
susceptibility</a>.
<em>Neuron</em>. 2022 Apr 6;110(7):1193-1210.e13.
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/35093191" target="_blank">35093191</a>; PMC: <a
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9810341/" target="_blank">PMC9810341</a>
</p>
<p>
Gabitto MI, Travaglini KJ, Rachleff VM, Kaplan ES, Long B, Ariza J, Ding Y, Mahoney JT, Dee N, Goldy
J <em>et al</em>.
<a href="https://doi.org/10.1038/s41593-024-01774-5" target="_blank">
Integrated multimodal cell atlas of Alzheimer's disease</a>.
<em>Nat Neurosci</em>. 2024 Dec;27(12):2366-2383.
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/39402379" target="_blank">39402379</a>; PMC: <a
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11614693/" target="_blank">PMC11614693</a>
</p>
<p>
Hawrylycz M, Kaplan ES, Travaglini KJ, Gabitto MI, Miller JA, Ng L, Close JL, Hodge RD, Long B,
Mollenkopf T <em>et al</em>.
<a href="https://doi.org/10.1038/s43587-024-00719-8" target="_blank">
SEA-AD is a multimodal cellular atlas and resource for Alzheimer's disease</a>.
<em>Nat Aging</em>. 2024 Oct;4(10):1331-1334.
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/39402332" target="_blank">39402332</a>; PMC: <a
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11577961/" target="_blank">PMC11577961</a>
</p>