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Updated: Jun 10, 2026
An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues
Published on: April 5, 2018
INSTINCT: Multi-sample integration of spatial chromatin accessibility sequencing data via stochastic domain
Yuyao Liu1, Zhen Li1, Xiaoyang Chen1
1Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing, 100084, China.
We developed INSTINCT, a new method for integrating multiple spatial ATAC-seq datasets. This approach effectively removes batch effects and noise, enabling deeper insights into epigenomic landscapes and regulatory processes.
Area of Science:
- Genomics
- Epigenetics
- Computational Biology
Background:
- Spatial epigenomic techniques like spATAC-seq offer simultaneous characterization of epigenomic heterogeneity and spatial information.
- Integrative analysis of multiple spATAC-seq samples is crucial for eliminating non-biological factors and exploring tissue structures.
- No established methods exist for multi-sample spATAC-seq integration.
Purpose of the Study:
- To present INSTINCT, a novel method for multi-sample integration of spatial chromatin accessibility sequencing data.
- To address the challenge of handling high dimensionality and eliminating noise/batch effects in spATAC-seq data.
- To facilitate comprehensive exploration of epigenomic landscapes and discovery of biological implications.
Main Methods:
- INSTINCT utilizes a stochastic domain translation procedure for multi-sample integration of spATAC-seq data.
- The method is designed to efficiently handle high-dimensional data and remove complex noise and batch effects.
- Validation was performed using simulated scenarios and real-world datasets.
Main Results:
- INSTINCT demonstrates superior and robust performance in integrating spATAC-seq data.
- The method effectively identifies spatial domains, aids in visualization, and facilitates spot-type annotation.
- INSTINCT supports various downstream analyses, including motif and expression enrichment, and partitioned heritability analysis.
Conclusions:
- INSTINCT provides a robust solution for multi-sample spATAC-seq data integration.
- The method enhances the exploration of spatial epigenomic landscapes and regulatory processes.
- INSTINCT offers significant advantages for spatial domain identification and downstream biological discovery.
