Using Chromatin Accessibility to Delineate Therapeutic Subtypes in Pancreatic Cancer Patient-Derived Cell Lines

Summary

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).

Graphical Abstract

Highlights

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  ATAC-seq protocol to measure chromatin accessibility in patient-derived cell lines

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  Includes detailed size selection library clean-up step

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  Instructions on how to calculate the library molarity using Agilent Bioanalyzer

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  A comprehensive data analysis pipeline is provided

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.