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REnformer, a single-cell ATAC-seq predicting model to investigate open chromatin sites
Riva SG +6 more
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Analytical Approaches for ATAC-seq Data Analysis
Current Protocols in Human Genetics, 2020 AbstractATAC‐seq, the assay for transposase‐accessible chromatin using sequencing, is a quick and efficient approach to investigating the chromatin accessibility landscape. Investigating chromatin accessibility has broad utility for answering many biological questions, such as mapping nucleosomes, identifying transcription factor binding sites, and ...
Nathan C. Sheffield, Jason P Smith
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Measuring Chromatin Accessibility: ATAC-Seq
2021Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq) is a method to investigate the accessibility of chromatin in a genome-wide fashion. In this chapter, we provide a brief history of the chromatin accessibility field followed by a detailed protocol to perform ATAC-Seq assay.
Sahu, Sanjeeb Kumar +2 more
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ATAC-Seq Optimization for Cancer Epigenetics Research
Journal of Visualized Experiments, 2022The assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) probes deoxyribonucleic acid (DNA) accessibility using the hyperactive Tn5 transposase. Tn5 cuts and ligates adapters for high-throughput sequencing within accessible chromatin regions. In eukaryotic cells, genomic DNA is packaged into chromatin, a complex of DNA,
Mikhala, Cooper +4 more
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2023
ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) has gained wide popularity as a fast, straightforward, and efficient way of generating genome-wide maps of open chromatin and guiding identification of active regulatory elements and inference of DNA protein binding locations.
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ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) has gained wide popularity as a fast, straightforward, and efficient way of generating genome-wide maps of open chromatin and guiding identification of active regulatory elements and inference of DNA protein binding locations.
openaire +2 more sources
An ATAC-seq protocol for neuroscience research
Anatomical Science InternationalATAC-seq (assay for transposase-accessible chromatin using sequencing) enables high resolution mapping of chromatin accessibility, providing critical insights into gene regulatory mechanisms in neuroscience research. This protocol presents an optimized approach for applying ATAC-seq to neural tissues and cells, addressing the unique challenges of ...
Nur Hasan, Prince +3 more
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Dissecting the Epigenome Driving Drug Resistance by ATAC-Seq
2022The transcription of each gene is tightly regulated by elements like promoters, enhancers, silencers and insulators. These elements determine the temporal and tissue-specific expression in development and disease. Drug resistance is the major obstacle in successfully treating cancer patients.
Francesca, de Nicola +2 more
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Prenet: Predictive network from ATAC-SEQ data
Journal of Bioinformatics and Computational Biology, 2020Assays for transposase-accessible chromatin sequencing (ATAC-seq) provides an innovative approach to study chromatin status in multiple cell types. Moreover, it is also possible to efficiently extract differentially accessible chromatin (DACs) regions by using state-of-the-art algorithms (e.g.
Nazmus Salehin +2 more
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Exploring the Cancer Immune Epigenome by ATAC-Seq
The Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is a rapid and sensitive method for exploring the cancer immune epigenome. ATAC-seq captures open chromatin sites based on transposing the sequencing adapter directly into native chromatin in vitro.Chunling, Zeng, Yuexiang, Wang
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