Explore regulatory landscapes
across mouse tissues.
Explore cell identities, marker-accessible regions, and chromatin regulatory patterns across nine mouse tissues.
Cell atlas / UMAP
Loading the validated local atlas file, if available.
Cell composition
Counts of cells currently selected, grouped by tissue. Changing tissue or cell type updates these counts.
Metacell composition
Select a SEACell to inspect its source-derived cells. SEACells may include multiple tissues and cell types; membership does not establish biological purity.
Cell-type marker accessible regions
Browse actual published BED intervals from the analysis repository. Coordinates are zero-based and half-open; these are peak intervals, not quantitative signal tracks.
| Chromosome | Start | End | Length (bp) | UCSC mm10 |
|---|---|---|---|---|
| Select a population to load intervals. | ||||
Compare two cell-type peak sets
This explores coordinate overlap of published marker intervals. Overlap does not establish differential accessibility, statistical significance, or common peak boundaries. Each input region is counted once if it overlaps at least one region in the other group.
Choose two cell types and run the comparison.
Gene activity explorer
Explore ATAC-derived gene activity, not RNA expression. Scores were exported from the original ArchR GeneScoreMatrix; standard ArchR default normalization is assumed from published code. Higher scores indicate greater ArchR-derived local accessibility signal, not expression or statistical significance.
Checking available gene activity…
Selected genes load on demand. Colors are capped at the 99th percentile of positive scores for visualization only; the original source values remain unchanged.
Nine tissue datasets
Explore the study's deposited tissue datasets through the GEO series. Original sequencing data and associated processed records are linked from GSE286329. Tissue-specific peak matrices should not be combined without peak harmonization.
About this atlas
The study profiles single-cell chromatin accessibility across nine mouse tissues, identifying tissue-specific regulatory programs in 28 major cell types. The atlas provides an interactive view of the study's processed accessibility data, precomputed cell identities, and selected gene-activity scores.
Paper: Chromatin accessibility landscapes define stromal cell identities across tissues · Communications Biology (2026).
Genome assembly: mm10. Gene activity is an ATAC-derived measure, not RNA expression. This study contains nine mouse-tissue single-cell ATAC-seq datasets; cross-sample feature integration requires common genomic intervals, not concatenation of tissue-specific peak matrices.
Download citation: BibTeX (.bib) · RIS (EndNote / Zotero) · PubMed.
Publication and reuse: Nooranikhojasteh A, Tavallaee G, Khuu N, et al. Chromatin accessibility landscapes define stromal cell identities across tissues. Communications Biology 9, 480 (2026). DOI. The published article is licensed under Creative Commons Attribution 4.0 (CC BY 4.0); credit the original authors, provide the license link and indicate adaptations. The atlas software is released under the MIT License; the curated files served under data/ are released under CC BY 4.0 with source attribution. These are separate grants from the published article license. The lab logo and externally linked resources are not relicensed.