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Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq
Published on: March 12, 2021
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Fundamental and practical approaches for single-cell ATAC-seq analysis
Peiyu Shi1, Yage Nie2, Jiawen Yang1
1State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China.
Abiotech
|October 31, 2022
Summary
This review provides a practical guide for processing single-cell ATAC-seq (scATAC-seq) data, covering quality control to downstream analysis. It highlights scATAC-seq applications in epigenomic profiling, variant function, and cell lineage tracing.
Area of Science:
- Genomics
- Epigenetics
- Single-cell analysis
Background:
- Transposase-accessible chromatin assays (ATAC-seq) map genome-wide chromatin accessibility.
- Single-cell ATAC-seq (scATAC-seq) measures open chromatin at the single-cell level for epigenetic regulation studies.
- scATAC-seq data is sparse and noisy, requiring specialized processing methods.
Purpose of the Study:
- To provide a practical guide for processing scATAC-seq data.
- To cover the entire workflow from quality evaluation to downstream analysis.
- To discuss diverse applications of scATAC-seq.
Main Methods:
- Review of existing scATAC-seq methodologies.
- Quality control and data processing strategies for sparse, noisy single-cell data.
- Downstream analysis techniques for epigenomic profiling and variant interpretation.
Main Results:
- Comprehensive overview of scATAC-seq data processing.
- Discussion on leveraging scATAC-seq for non-coding variant function investigation.
- Exploration of using scATAC-seq by-products for copy number variant inference and cell lineage tracing.
Conclusions:
- This review serves as a practical resource for researchers using scATAC-seq.
- It aims to facilitate the design and implementation of scATAC-seq assays.
- The guide supports diverse research fields by enhancing scATAC-seq data utilization.
