Emerging Approaches to Profile Accessible Chromatin from Ffpe Sections Article Swipe
Vishnu Udayakumar Sunita Kumary
,
Bryan J. Venters
,
Raman Karthikeyan
,
Sagnik Sen
,
Pierre‐Olivier Estève
,
Martis W. Cowles
,
Michael‐Christopher Keogh
,
Sriharsa Pradhan
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.20944/preprints202402.1301.v1
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.20944/preprints202402.1301.v1
Nucleosomes are non-uniformly distributed across eukarytic genomes, with stretches of ‘open’ chromatin strongly associated with transcriptionally active promoters and enhancers. Understanding chromatin accessibility patterns in normal tissue and how they are altered in pathologies can provide critical insights to development and disease. With the advent of high-throughput sequencing, a variety of strategies have been devised to identify open regions across the genome, including DNase-seq, MNase-seq, FAIRE-seq, ATAC-seq, and NicE-seq. However, the broad application of such methods to FFPE (formalin-fixed paraffin embedded) tissues has been curtailed by the major technical challenges imposed by highly fixed and damaged genomic material. Here we review the most common approaches for mapping open chromatin regions, recent optimizations to overcome the challenges of working with FFPE tissue, and a brief overview of a typical data pipeline with analysis considerations.
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Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.20944/preprints202402.1301.v1
- https://www.preprints.org/manuscript/202402.1301/v1/download
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All OpenAlex metadata
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https://doi.org/10.20944/preprints202402.1301.v1Digital Object Identifier
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Emerging Approaches to Profile Accessible Chromatin from Ffpe SectionsWork title
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preprintOpenAlex work type
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enPrimary language
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2024Year of publication
- Publication date
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2024-02-23Full publication date if available
- Authors
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Vishnu Udayakumar Sunita Kumary, Bryan J. Venters, Raman Karthikeyan, Sagnik Sen, Pierre‐Olivier Estève, Martis W. Cowles, Michael‐Christopher Keogh, Sriharsa PradhanList of authors in order
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https://doi.org/10.20944/preprints202402.1301.v1Publisher landing page
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https://www.preprints.org/manuscript/202402.1301/v1/downloadDirect link to full text PDF
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YesWhether a free full text is available
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greenOpen access status per OpenAlex
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https://www.preprints.org/manuscript/202402.1301/v1/downloadDirect OA link when available
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Chromatin, Computational biology, Computer science, Biology, Genetics, DNATop concepts (fields/topics) attached by OpenAlex
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1Total citation count in OpenAlex
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2024: 1Per-year citation counts (last 5 years)
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10Other works algorithmically related by OpenAlex
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