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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.
STAR Protocols
|October 28, 2020
Summary
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.
