ReviewMethods in cell biology2019
Genome-wide analysis of chromatin accessibility using ATAC-seq.
Review in Methods in cell biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
36 citing papers in PubMed, 78 citations in OpenAlex.
- Multi-omics data-based modeling reveals tumorigenesis- and prognosis-associated genes with clinical potential in lung adenocarcinoma.BMC cancer · 2025Article
- Transcriptional and epigenetic rewiring by the NUP98::KDM5A fusion oncoprotein directly activates CDK12.Nature communications · 2025Article
- Integrative multi-omics data provide insights into the biosynthesis of furanocoumarins and mechanisms regulating their accumulation in Angelica dahurica.Communications biology · 2025Article
- Integrative analysis of gene expression and chromatin dynamics multi-omics data in mouse models of bleomycin-induced lung fibrosis.Epigenetics & chromatin · 2025Article
- Integrative ATAC-seq and RNA-seq Analysis of the Longissimus Dorsi Muscle of Gannan Yak and Jeryak.International journal of molecular sciences · 2024Article
- Transcription of microRNAs is regulated by developmental signaling pathways and transcription factors.Frontiers in cell and developmental biology · 2024Article
- Establishing an optimized ATAC-seq protocol for the maize.Frontiers in plant science · 2024Article
- PlantCADB: A Comprehensive Plant Chromatin Accessibility Database.Genomics, proteomics & bioinformatics · 2023Article
- Integrative epigenome profiling of 47XXY provides insights into whole genomic DNA hypermethylation and active chromatin accessibility.Frontiers in molecular biosciences · 2023Article
- Single cell cortical bone transcriptomics define novel osteolineage gene sets altered in chronic kidney disease.Frontiers in endocrinology · 2023Article
- GAGAM v1.2: An Improvement on Peak Labeling and Genomic Annotated Gene Activity Matrix Construction.Genes · 2022Article
- A chromatin accessibility landscape during early adipogenesis of human adipose-derived stem cells.Adipocyte · 2022Article
- A nuclear cAMP microdomain suppresses tumor growth by Hippo pathway inactivation.Cell reports · 2022Article
- Protocol for single-nucleus ATAC sequencing and bioinformatic analysis in frozen human brain tissue.STAR protocols · 2022Article
- The Genomics of Auditory Function and Disease.Annual review of genomics and human genetics · 2022Review
- Sample-multiplexing approaches for single-cell sequencing.Cellular and molecular life sciences : CMLS · 2022Review
- Review
- Characterization of chromatin accessibility in psoriasis.Frontiers of medicine · 2022Article
- The FUS::DDIT3 fusion oncoprotein inhibits BAF complex targeting and activity in myxoid liposarcoma.Molecular cell · 2022Article
- Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Programs of gene transcription are controlled by cis-acting DNA elements, including enhancers, silencers, and promoters. Local accessibility of chromatin has proven to be a highly informative structural feature for identifying such regulatory elements, which tend to be relatively open due to their interactions with proteins. Recently, ATAC-seq (assay for transposase-accessible chromatin using sequencing) has emerged as one of the most powerful approaches for genome-wide chromatin accessibility profiling. This method assesses DNA accessibility using hyperactive Tn5 transposase, which simultaneously cuts DNA and inserts sequencing adaptors, preferentially in regions of open chromatin. ATAC-seq is a relatively simple procedure which can be applied to only a few thousand cells. It is well-suited to developing embryos of sea urchins and other echinoderms, which are a prominent experimental model for understanding the genomic control of animal development. In this chapter, we present a protocol for applying ATAC-seq to embryonic cells of sea urchins.
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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.