The 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, China.
Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences & MOE Key Lab of Rare Pediatric Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
Nucleic Acids Res. 2024 Jan 5;52(D1):D285-D292. doi: 10.1093/nar/gkad924.
Chromatin accessibility profiles at single cell resolution can reveal cell type-specific regulatory programs, help dissect highly specialized cell functions and trace cell origin and evolution. Accurate cell type assignment is critical for effectively gaining biological and pathological insights, but is difficult in scATAC-seq. Hence, by extensively reviewing the literature, we designed scATAC-Ref (https://bio.liclab.net/scATAC-Ref/), a manually curated scATAC-seq database aimed at providing a comprehensive, high-quality source of chromatin accessibility profiles with known cell labels across broad cell types. Currently, scATAC-Ref comprises 1 694 372 cells with known cell labels, across various biological conditions, >400 cell/tissue types and five species. We used uniform system environment and software parameters to perform comprehensive downstream analysis on these chromatin accessibility profiles with known labels, including gene activity score, TF enrichment score, differential chromatin accessibility regions, pathway/GO term enrichment analysis and co-accessibility interactions. The scATAC-Ref also provided a user-friendly interface to query, browse and visualize cell types of interest, thereby providing a valuable resource for exploring epigenetic regulation in different tissues and cell types.
单细胞分辨率下的染色质可及性图谱可以揭示细胞类型特异性的调控程序，有助于剖析高度专业化的细胞功能，并追踪细胞的起源和进化。准确的细胞类型分配对于有效地获得生物学和病理学见解至关重要，但在 scATAC-seq 中却很困难。因此，我们通过广泛查阅文献，设计了 scATAC-Ref（https://bio.liclab.net/scATAC-Ref/），这是一个手动整理的 scATAC-seq 数据库，旨在提供一个全面、高质量的带有已知细胞标签的染色质可及性图谱资源，涵盖广泛的细胞类型。目前，scATAC-Ref 包含 1 694 372 个具有已知细胞标签的细胞，涵盖了各种生物学条件、>400 种细胞/组织类型和 5 个物种。我们使用统一的系统环境和软件参数，对这些具有已知标签的染色质可及性图谱进行了全面的下游分析，包括基因活性评分、TF 富集评分、差异染色质可及性区域、通路/GO 术语富集分析和共可及性相互作用。scATAC-Ref 还提供了一个用户友好的界面，用于查询、浏览和可视化感兴趣的细胞类型，从而为探索不同组织和细胞类型中的表观遗传调控提供了有价值的资源。
