ArticleMethods in molecular biology (Clifton, N.J.)2023
Genome-Wide Mapping of Active Regulatory Elements Using ATAC-seq.
Article in Methods in molecular biology (Clifton, N.J.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 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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Who cites it
9 citing papers in PubMed, 11 citations in OpenAlex.
- Age-related microbiome metabolites alter RNA splicing and chromatin accessibility in the brain.bioRxiv : the preprint server for biology · 2025Article
- DNASE1L3 surveils mitochondrial DNA on the surface of distinct mammalian cells.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
- Chromatin accessibility provides a window into the genetic etiology of human brain disease.Trends in genetics : TIG · 2025Review
- 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
- Machine learning tools for deciphering the regulatory logic of enhancers in health and disease.Frontiers in genetics · 2025Review
- Genome-wide distribution of 5-hydroxymethyluracil and chromatin accessibility in the Breviolum minutum genome.Genome biology · 2024Article
- Genome-wide distribution of 5-hydroxymethyluracil and chromatin accessibility in thebioRxiv : the preprint server for biology · 2023Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Active cis-regulatory elements (cREs) in eukaryotes are characterized by nucleosomal depletion and, accordingly, higher accessibility. This property has turned out to be immensely useful for identifying cREs genome-wide and tracking their dynamics across different cellular states and is the basis of numerous methods taking advantage of the preferential enzymatic cleavage/labeling of accessible DNA. ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) has emerged as the most versatile and widely adaptable method and has been widely adopted as the standard tool for mapping open chromatin regions. Here, we discuss the current optimal practices and important considerations for carrying out ATAC-seq experiments, primarily in the context of mammalian systems.
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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 OpenQuestion graph.