ArticleScientific data2019
An ATAC-seq atlas of chromatin accessibility in mouse tissues.
Article in Scientific data, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers, 1 of them a synthesis that pooled it.
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Who cites it
77 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Learning single-cell chromatin accessibility profiles using meta-analytic marker genes.Briefings in bioinformatics · 2023Pooled it
- UnlockingNAR genomics and bioinformatics · 2026Article
- Chromatin Accessibility Reveals Adaptive Regulatory Variation in a Keystone Freshwater Fish.Molecular ecology · 2026Article
- Challenges in predicting chromatin accessibility differences between species.NAR genomics and bioinformatics · 2026Article
- Article
- Conversion of Transplanted Mature Hepatocytes into AfpAdvanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Chromatin accessibility landscapes define stromal cell identities across tissues.Communications biology · 2026Article
- ChromAcS: an automated and flexible GUI for end-to-end reproducible ATAC-seq analysis across multiple species.BMC bioinformatics · 2026Article
- Integrated chromatin and transcriptomic profiling reveals sex-specific mechanisms of gene regulation in hepatic nutrient responses.PLoS biology · 2026Article
- Developing a comprehensive database and search tool for single-cell ATAC-seq data.Scientific reports · 2026Article
- Integrated RNA-seq and ATAC-seq analyses reveal muscle development differences between european meat pigeon and shiqi pigeon during embryonic to post-hatching stages.Frontiers in cell and developmental biology · 2026Article
- Challenges in Predicting Chromatin Accessibility Differences between Species.bioRxiv : the preprint server for biology · 2025Article
- ATAC-seq in Emerging Model Organisms: Challenges and Strategies.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2025Review
- REV-ERBα regulates brain NADNature aging · 2025Article
- Tissue-Specific Chromatin Accessibility Regions and Transcription Factor Binding Sites in Pig Brain and Endocrine Tissues.Molecular neurobiology · 2025Article
- Igf2 adult-specific skeletal muscle enhancer activity revealed in mice with intergenic CTCF boundary deletion.PLoS genetics · 2025Article
- Hepatic Inactivation of Carnitine Palmitoyltransferase 1a Lowers ApoB-Containing Lipoproteins in Mice.Arteriosclerosis, thrombosis, and vascular biology · 2025Article
- Prediction of local convergent shifts in evolutionary rates with phyloConverge.Bioinformatics (Oxford, England) · 2025Article
- Mapping the transcriptional and epigenetic landscape of organotypic endothelial diversity in the developing and adult mouse.Nature cardiovascular research · 2025Article
- scRNA-seq and scATAC-seq analyses highlight the role of TNF signaling pathway in chronic obstructive pulmonary disease model mice.PloS one · 2025Article
17 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
19 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is a fundamental epigenomics approach and has been widely used in profiling the chromatin accessibility dynamics in multiple species. A comprehensive reference of ATAC-seq datasets for mammalian tissues is important for the understanding of regulatory specificity and developmental abnormality caused by genetic or environmental alterations. Here, we report an adult mouse ATAC-seq atlas by producing a total of 66 ATAC-seq profiles from 20 primary tissues of both male and female mice. The ATAC-seq read enrichment, fragment size distribution, and reproducibility between replicates demonstrated the high quality of the full dataset. We identified a total of 296,574 accessible elements, of which 26,916 showed tissue-specific accessibility. Further, we identified key transcription factors specific to distinct tissues and found that the enrichment of each motif reflects the developmental similarities across tissues. In summary, our study provides an important resource on the mouse epigenome and will be of great importance to various scientific disciplines such as development, cell reprogramming, and genetic disease.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.