ReviewMethods in molecular biology (Clifton, N.J.)2021
Interrogating the Accessible Chromatin Landscape of Eukaryote Genomes Using ATAC-seq.
Review in Methods in molecular biology (Clifton, N.J.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
20 citing papers in PubMed.
- Single-Cell CRISPR: An Efficient Strategy for Decoding Plant Cis-Regulatory Complexity.Plant biotechnology journal · 2026Review
- Multi-omics data-based modeling reveals tumorigenesis- and prognosis-associated genes with clinical potential in lung adenocarcinoma.BMC cancer · 2025Article
- Age-related microbiome metabolites alter RNA splicing and chromatin accessibility in the brain.bioRxiv : the preprint server for biology · 2025Article
- Sensitive, direct detection of non-coding off-target base editor unwinding and editing in primary cells.bioRxiv : the preprint server for biology · 2025Article
- Comprehensive analysis of m6A-seq data reveals distinct features of conserved and unique m6A sites in mammals.RNA (New York, N.Y.) · 2025Article
- Mapping the Simultaneously Accessible and ssDNA-Containing Genome With KAS-ATAC Sequencing.Bio-protocol · 2025Article
- KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome.Genome research · 2025Article
- The chromatin landscape of the histone-possessingGenome research · 2025Article
- Genome-wide distribution of 5-hydroxymethyluracil and chromatin accessibility in the Breviolum minutum genome.Genome biology · 2024Article
- Differential Regulation of Male-Hormones-Related Enhancers Revealed by Chromatin Accessibility and Transcriptional Profiles in Pig Liver.Biomolecules · 2024Article
- The chromatin landscape of the euryarchaeon Haloferax volcanii.Genome biology · 2023Article
- The landscape of the histone-organized chromatin of Bdellovibrionota bacteria.bioRxiv : the preprint server for biology · 2023Article
- Genome-wide distribution of 5-hydroxymethyluracil and chromatin accessibility in thebioRxiv : the preprint server for biology · 2023Article
- CasKAS: direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA mapping.Genome biology · 2023Article
- Which field of research would Gregor Mendel choose in the 21st century?The Plant cell · 2022Review
- Investigating chromatin accessibility during development and differentiation by ATAC-sequencing to guide the identification of cis-regulatory elements.Biochemical Society transactions · 2022Article
- Whole-genome methods to define DNA and histone accessibility and long-range interactions in chromatin.Biochemical Society transactions · 2022Review
- Advancements in Genomic and Behavioral Neuroscience Analysis for the Study of Normal and Pathological Brain Function.Frontiers in molecular neuroscience · 2022Review
- An optimized ATAC-seq protocol for genome-wide mapping of active regulatory elements in primary mouse cortical neurons.STAR protocols · 2021Article
- Regulatory SNPs: Altered Transcription Factor Binding Sites Implicated in Complex Traits and Diseases.International journal of molecular sciences · 2021Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The ATAC-seq assay has emerged as the most useful, versatile, and widely adaptable method for profiling accessible chromatin regions and tracking the activity of cis-regulatory elements (cREs) in eukaryotes. Thanks to its great utility, it is now being applied to map active chromatin in the context of a very wide diversity of biological systems and questions. In the course of these studies, considerable experience working with ATAC-seq data has accumulated and a standard set of computational tasks that need to be carried for most ATAC-seq analyses has emerged. Here, we review and provide examples of common such analytical procedures (including data processing, quality control, peak calling, identifying differentially accessible open chromatin regions, and variable transcription factor (TF) motif accessibility) and discuss recommended optimal practices.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.