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Using Chromatin Accessibility to Delineate Therapeutic Subtypes in Pancreatic Cancer Patient-Derived Cell Lines
Holly Brunton1,2, Ian M Garner3, Ulla-Maja Bailey2
1Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, UK.
Abstract:
Disrupted chromatin regulatory processes contribute to the development of cancer, in particular pancreatic ductal adenocarcinoma. The assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) is typically used to study chromatin organization. Here, we present a revised ATAC-seq protocol to study chromatin accessibility in adherent patient-derived cell lines. We provide details on how to calculate the library molarity using Agilent's Bioanalyzer and an analysis pipeline for peak calling and transcription factor mapping. For complete details on the use and execution of this protocol, please refer to Brunton et al. (2020).
Insights
This study refines the assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) for analyzing chromatin accessibility in pancreatic cancer cell lines. The improved protocol aids in understanding cancer development by examining chromatin organization.
Area of Science:
- Genomics
- Cancer Biology
- Molecular Biology
Background:
- Disrupted chromatin regulation is implicated in cancer, particularly pancreatic ductal adenocarcinoma.
- Assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) is a key technique for studying chromatin organization.
Purpose of the Study:
- To present a revised ATAC-seq protocol optimized for adherent patient-derived cell lines.
- To provide detailed methods for library molarity calculation and data analysis.
Main Methods:
- Revision of the standard ATAC-seq protocol.
- Utilizing Agilent's Bioanalyzer for library molarity assessment.
- Implementation of an analysis pipeline for peak calling and transcription factor mapping.
Main Results:
- A refined ATAC-seq protocol for chromatin accessibility studies in patient-derived cell lines.
- Detailed guidance on library quantification and bioinformatics analysis.
Conclusions:
- The revised ATAC-seq protocol facilitates the study of chromatin accessibility in pancreatic cancer models.
- This methodology supports research into the role of chromatin regulation in cancer development.
