ArticleScientific reports2019
High Quality ATAC-Seq Data Recovered from Cryopreserved Breast Cell Lines and Tissue.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers, 1 of them a synthesis that pooled it.
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Who cites it
27 citing papers in PubMed, 1 synthesis or guideline pooled it, 33 citations in OpenAlex.
- Towards a consensus atlas of human and mouse adipose tissue at single-cell resolution.Nature metabolism · 2025Guideline
- ATAC-seq of low-input and cryopreserved primordial germ cells reveals functional enhancers.Development (Cambridge, England) · 2026Article
- Coordinated Temporal Dynamics of Glucocorticoid Receptor Binding and Chromatin Landscape Drive Transcriptional Regulation.bioRxiv : the preprint server for biology · 2026Article
- Integrated multiomics analysis reveals the molecular features and crucial regulators of hair follicles in yak (Bos grunniens).Communications biology · 2026Article
- Assay for Transposase-Accessible Chromatin Sequencing (ATAC-seq) of Cancer Cells in Culture.Methods in molecular biology (Clifton, N.J.) · 2026Article
- IKAROS Gene Regulatory Network Reveal ERG as a Vulnerability in B-cell Acute Lymphoblastic Leukemia.bioRxiv : the preprint server for biology · 2025Article
- ATAC-seq in Emerging Model Organisms: Challenges and Strategies.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2025Review
- Capturing Chromatin Organization by MNase-seq and ATAC-seq.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Histone variant H2AZ1 drives lung cancer progression through the RELA-HIF1A-EGFR signaling pathway.Cell communication and signaling : CCS · 2024Article
- Iterative assay for transposase-accessible chromatin by sequencing to isolate functionally relevant neuronal subtypes.Science advances · 2024Article
- DisP-seq reveals the genome-wide functional organization of DNA-associated disordered proteins.Nature biotechnology · 2024Article
- Parallel recovery of chromatin accessibility and gene expression dynamics from frozen human regulatory T cells.Scientific reports · 2023Article
- HIV vaccine candidate efficacy in female macaques mediated by cAMP-dependent efferocytosis and V2-specific ADCC.Nature communications · 2023Article
- Practical Considerations for Single-Cell Genomics.Current protocols · 2022Review
- ATAC-seq Optimization for Cancer Epigenetics Research.Journal of visualized experiments : JoVE · 2022Article
- Chromatin accessibility profiling by ATAC-seq.Nature protocols · 2022Review
- ATAC Sequencing Protocol For Cryopreserved Mammalian Cells.Bio-protocol · 2022Article
- Dynamic transcriptome and chromatin architecture in granulosa cells during chicken folliculogenesis.Nature communications · 2022Article
- Nuclear pore protein NUP210 depletion suppresses metastasis through heterochromatin-mediated disruption of tumor cell mechanical response.Nature communications · 2021Article
- Dual detection of chromatin accessibility and DNA methylation using ATAC-Me.Nature protocols · 2021Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
DNA accessibility to transcription regulators varies between cells and modulates gene expression patterns. Several "open" chromatin profiling methods that provide valuable insight into the activity of these regulatory regions have been developed. However, their application to clinical samples has been limited despite the discovery that the Analysis of Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) method can be performed using fewer cells than other techniques. Obtaining fresh rather than stored samples and a lack of adequate optimization and quality controls are major barriers to ATAC's clinical implementation. Here, we describe an optimized ATAC protocol in which we varied nuclear preparation conditions and transposase concentrations and applied rigorous quality control measures before testing fresh, flash frozen, and cryopreserved breast cells and tissue. We obtained high quality data from small cell number. Furthermore, the genomic distribution of sequencing reads, their enrichment at transcription start sites, and transcription factor footprint analyses were similar between cryopreserved and fresh samples. This updated method is applicable to clinical samples, including cells from fine needle aspiration and tissues obtained via core needle biopsy or surgery. Chromatin accessibility analysis using patient samples will greatly expand the range of translational research and personalized medicine by identification of clinically-relevant epigenetic features.
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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.