Journal
STAR PROTOCOLS
Volume 1, Issue 2, Pages -Publisher
ELSEVIER
DOI: 10.1016/j.xpro.2020.100079
Keywords
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Funding
- National Health and Medical Research Council of Australia (NHMRC) [631701, A29996, 103721/Z/14/Z]
- American Association for Cancer Research (AACR) Landon Foundation - INNOVATOR Award
- NIH
- NHMRC
- Cancer Australia
- Cancer Research UK
- Wellcome Trust Senior Investigator Award
- Pancreatic Cancer UK Future Research Leaders Fund
- Scottish Genome Partnership
- Pancreatic Cancer Research Fund [FLF2015_04_Glasgow, SEHHD-CSO 1175759/2158447, RBAP10AHJB, 12182]
- MRC/EPSRC Glasgow Molecular Pathology Node [602783, FIMP-CUP_J33G13000210001]
- Howat Foundation
- Italian Cancer Genome Project - Ministry of University (FIRB)
- Associazione Italiana Ricerca Cancro
- FP7 European Community Grant Cam-Pac
- Italian Ministry of Health
- ICGC Ontario Institute for Cancer Research
- [427601]
- [535903]
- [CA62924]
- [5R01CA150190-07]
- [P50 CA102701]
- [U01 CA224145]
- [1162860]
- [1162556]
- [1143699]
- [C29717/A17263]
- [C29717/A18484]
- [C596/A18076]
- [C596/A20921]
- [A23526]
- [A14276]
- [A25233]
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Disrupted chromatin regulatory processes contribute to the development of can-cer, 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 pro-tocol 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).
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