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Peer-reviewedCC BY-NC 4.0Nucleic Acids Research

OSCAR: an omics atlas of paired single-cell ATAC-seq and RNA-seq for decoding cell-specific gene regulation

  • Chao Song1,2
  • Yao Zhou2
  • Chenchen Feng2
  • Xintong Dai1
  • Jiaxin Xiao1
  • Xuan Fan3
  • Kewei Wang2
  • Pengxiang Xiao2
  • Yixin Zheng2
  • Wenxi Luo2
  • Chunquan Li1,2,3,4,5
  • Qiuyu Wang1,2
5 affiliations
  1. 1The First Affiliated Hospital & Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases, Hengyang Medical School, University of South China , Hengyang, Hunan 421001 ,
  2. 2School of Computer, University of South China , Hengyang, Hunan 421001 ,
  3. 3School of Traditional Chinese Medicine, Beijing University of Chinese Medicine , Beijing 100029 ,
  4. 4National Health Commission Key Laboratory of Birth Defect Research and Prevention & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China , Hengyang, Hunan 421001 ,
  5. 5NHC Key Laboratory of Neurodegenerative Diseases, University of South China , Hengyang 421001 ,
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Abstract

Paired single-cell chromatin accessibility and transcriptome profiles provide a powerful framework for dissecting cell-specific regulatory programs underlying diverse biological processes and human diseases. The rapid accumulation of paired single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) and single-cell RNA sequencing (scRNA-seq) data has led to an urgent need to comprehensively integrate these data to illustrate the regulatory landscape at single-cell resolution. To address this need, we developed OSCAR (an Omics atlas of paired Single-Cell ATAC and RNA-seq, https://bio.liclab.net/OSCAR/) to curate large-scale paired scATAC-seq and scRNA-seq data and to provide comprehensive regulatory annotations and analyses. The current version of OSCAR catalogs 7749 898 human cells from 1136 samples across 30 tissue types. Importantly, OSCAR integrates paired scATAC-seq and scRNA-seq profiles for joint cell clustering and peak-to-gene linkage identification, and provides detailed (epi)genetic annotations for marker peaks and regulatory elements of marker genes, including super-enhancers, enhancers, enhancer RNAs (eRNAs), common and risk single nucleotide polymorphisms, expression quantitative trait loci, transcription factor binding sites, transcription factor/transcription co-factor binding peaks, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 target sites, DNase I hypersensitivity sites, chromatin accessibility regions, DNA methylation sites, chromatin interaction regions, and topologically associating domains. Furthermore, OSCAR provides three online analysis tools, including cell type enrichment analysis, sequence-based peak regulatory analysis, and peak-to-gene linkage analysis. Hence, OSCAR is a useful platform to query, browse, analyze, and visualize cell-specific regulatory programs across diverse human tissues and diseases.

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Cite

BibTeXRIS
BibTeX
@article{song2026oscar,
  title = {{OSCAR: an omics atlas of paired single-cell ATAC-seq and RNA-seq for decoding cell-specific gene regulation}},
  author = {Chao Song and Yao Zhou and Chenchen Feng and Xintong Dai and Jiaxin Xiao and Xuan Fan and Kewei Wang and Pengxiang Xiao and Yixin Zheng and Wenxi Luo and Chunquan Li and Qiuyu Wang},
  journal = {Nucleic Acids Research},
  year = {2026},
  month = oct,
  doi = {10.1093/nar/gkag1033},
  url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1033/9002627},
  note = {CC BY-NC 4.0},
}
RIS
TY  - JOUR
TI  - OSCAR: an omics atlas of paired single-cell ATAC-seq and RNA-seq for decoding cell-specific gene regulation
AU  - Chao Song
AU  - Yao Zhou
AU  - Chenchen Feng
AU  - Xintong Dai
AU  - Jiaxin Xiao
AU  - Xuan Fan
AU  - Kewei Wang
AU  - Pengxiang Xiao
AU  - Yixin Zheng
AU  - Wenxi Luo
AU  - Chunquan Li
AU  - Qiuyu Wang
PY  - 2026
DA  - 2026/10/27
JO  - Nucleic Acids Research
DO  - 10.1093/nar/gkag1033
UR  - https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1033/9002627
AB  - Paired single-cell chromatin accessibility and transcriptome profiles provide a powerful framework for dissecting cell-specific regulatory programs underlying diverse biological processes and human diseases. The rapid accumulation of paired single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) and single-cell RNA sequencing (scRNA-seq) data has led to an urgent need to comprehensively integrate these data to illustrate the regulatory landscape at single-cell resolution. To address this need, we developed OSCAR (an Omics atlas of paired Single-Cell ATAC and RNA-seq, https://bio.liclab.net/OSCAR/) to curate large-scale paired scATAC-seq and scRNA-seq data and to provide comprehensive regulatory annotations and analyses. The current version of OSCAR catalogs 7749 898 human cells from 1136 samples across 30 tissue types. Importantly, OSCAR integrates paired scATAC-seq and scRNA-seq profiles for joint cell clustering and peak-to-gene linkage identification, and provides detailed (epi)genetic annotations for marker peaks and regulatory elements of marker genes, including super-enhancers, enhancers, enhancer RNAs (eRNAs), common and risk single nucleotide polymorphisms, expression quantitative trait loci, transcription factor binding sites, transcription factor/transcription co-factor binding peaks, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 target sites, DNase I hypersensitivity sites, chromatin accessibility regions, DNA methylation sites, chromatin interaction regions, and topologically associating domains. Furthermore, OSCAR provides three online analysis tools, including cell type enrichment analysis, sequence-based peak regulatory analysis, and peak-to-gene linkage analysis. Hence, OSCAR is a useful platform to query, browse, analyze, and visualize cell-specific regulatory programs across diverse human tissues and diseases.
SN  - 0305-1048
SN  - 1362-4962
ER  -