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Title
Chromatin accessibility profiling by ATAC-seq
Authors
Keywords
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Journal
Nature Protocols
Volume -, Issue -, Pages -
Publisher
Springer Science and Business Media LLC
Online
2022-04-28
DOI
10.1038/s41596-022-00692-9
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Note: Only part of the references are listed.- Nuclei isolation of multiple brain cell types for omics interrogation
- (2021) Alexi Nott et al. Nature Protocols
- Nucleosome Positioning and Spacing: From Mechanism to Function
- (2021) Ashish Kumar Singh et al. JOURNAL OF MOLECULAR BIOLOGY
- ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis
- (2021) Jeffrey M. Granja et al. NATURE GENETICS
- Interpreting type 1 diabetes risk with genetics and single-cell epigenomics
- (2021) Joshua Chiou et al. NATURE
- Single-cell CUT&Tag analysis of chromatin modifications in differentiation and tumor progression
- (2021) Steven J. Wu et al. NATURE BIOTECHNOLOGY
- Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues
- (2021) Marek Bartosovic et al. NATURE BIOTECHNOLOGY
- Transcription factor chromatin profiling genome-wide using uliCUT&RUN in single cells and individual blastocysts
- (2021) Benjamin J. Patty et al. Nature Protocols
- Simultaneous trimodal single-cell measurement of transcripts, epitopes, and chromatin accessibility using TEA-seq
- (2021) Elliott Swanson et al. eLife
- Single-Cell Epigenomics and Functional Fine-Mapping of Atherosclerosis GWAS Loci
- (2021) Tiit Örd et al. CIRCULATION RESEARCH
- Profiling chromatin accessibility in formalin-fixed paraffin-embedded samples
- (2021) Vamsi Krishna Polavarapu et al. GENOME RESEARCH
- Dysregulation of brain and choroid plexus cell types in severe COVID-19
- (2021) Andrew C. Yang et al. NATURE
- The nf-core framework for community-curated bioinformatics pipelines
- (2020) Philip A. Ewels et al. NATURE BIOTECHNOLOGY
- Methods for ChIP-seq analysis: A practical workflow and advanced applications
- (2020) Ryuichiro Nakato et al. METHODS
- Quantification, Dynamic Visualization, and Validation of Bias in ATAC-Seq Data with ataqv
- (2020) Peter Orchard et al. Cell Systems
- Comparison of differential accessibility analysis strategies for ATAC-seq data
- (2020) Paul Gontarz et al. Scientific Reports
- The Human and Mouse Enteric Nervous System at Single-Cell Resolution
- (2020) Eugene Drokhlyansky et al. CELL
- Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer’s and Parkinson’s diseases
- (2020) M. Ryan Corces et al. NATURE GENETICS
- Mapping the epigenomic and transcriptomic interplay during memory formation and recall in the hippocampal engram ensemble
- (2020) Asaf Marco et al. NATURE NEUROSCIENCE
- Efficient low-cost chromatin profiling with CUT&Tag
- (2020) Hatice S. Kaya-Okur et al. Nature Protocols
- Chromatin integration labeling for mapping DNA-binding proteins and modifications with low input
- (2020) Tetsuya Handa et al. Nature Protocols
- ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation
- (2020) Mette Bentsen et al. Nature Communications
- Universal NicE-seq for high-resolution accessible chromatin profiling for formaldehyde-fixed and FFPE tissues
- (2020) Hang Gyeong Chin et al. Clinical Epigenetics
- Chromatin accessibility landscapes of skin cells in systemic sclerosis nominate dendritic cells in disease pathogenesis
- (2020) Qian Liu et al. Nature Communications
- Chromatin accessibility and the regulatory epigenome
- (2019) Sandy L. Klemm et al. NATURE REVIEWS GENETICS
- Low-input chromatin profiling in Arabidopsis endosperm using CUT&RUN
- (2019) Xiao-yu Zheng et al. Plant Reproduction
- High Quality ATAC-Seq Data Recovered from Cryopreserved Breast Cell Lines and Tissue
- (2019) Saori Fujiwara et al. Scientific Reports
- Single-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification
- (2019) Wai Lim Ku et al. NATURE METHODS
- Combined chemosensitivity and chromatin profiling prioritizes drug combinations in CLL
- (2019) Christian Schmidl et al. Nature Chemical Biology
- Profiling of Pluripotency Factors in Single Cells and Early Embryos
- (2019) Sarah J. Hainer et al. CELL
- Activation of PDGF pathway links LMNA mutation to dilated cardiomyopathy
- (2019) Jaecheol Lee et al. NATURE
- Epigenetic programming underpins B cell dysfunction in human SLE
- (2019) Christopher D. Scharer et al. NATURE IMMUNOLOGY
- RNA sequencing: the teenage years
- (2019) Rory Stark et al. NATURE REVIEWS GENETICS
- HMMRATAC: a Hidden Markov ModeleR for ATAC-seq
- (2019) Evan D Tarbell et al. NUCLEIC ACIDS RESEARCH
- PAN-INTACT enables direct isolation of lineage-specific nuclei from fibrous tissues
- (2019) Samadrita Bhattacharyya et al. PLoS One
- Pancreatic islet chromatin accessibility and conformation reveals distal enhancer networks of type 2 diabetes risk
- (2019) William W. Greenwald et al. Nature Communications
- CUT&Tag for efficient epigenomic profiling of small samples and single cells
- (2019) Hatice S. Kaya-Okur et al. Nature Communications
- Isolated C. elegans germ nuclei exhibit distinct genomic profiles of histone modification and gene expression
- (2019) Mei Han et al. BMC GENOMICS
- Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion
- (2019) Ansuman T. Satpathy et al. NATURE BIOTECHNOLOGY
- Landscape of stimulation-responsive chromatin across diverse human immune cells
- (2019) Diego Calderon et al. NATURE GENETICS
- CoBATCH for High-Throughput Single-Cell Epigenomic Profiling
- (2019) Qianhao Wang et al. MOLECULAR CELL
- Brain cell type–specific enhancer–promoter interactome maps and disease-risk association
- (2019) Alexi Nott et al. SCIENCE
- Mapping histone modifications in low cell number and single cells using antibody-guided chromatin tagmentation (ACT-seq)
- (2019) Benjamin Carter et al. Nature Communications
- Genome-wide profiling of nucleosome position and chromatin accessibility in single cells using scMNase-seq
- (2019) Weiwu Gao et al. Nature Protocols
- Quantification of Differential Transcription Factor Activity and Multiomics-Based Classification into Activators and Repressors: diffTF
- (2019) Ivan Berest et al. Cell Reports
- An atlas of chromatin accessibility in the adult human brain
- (2018) John F. Fullard et al. GENOME RESEARCH
- Genetic determinants of co-accessible chromatin regions in activated T cells across humans
- (2018) Rachel E. Gate et al. NATURE GENETICS
- Targeted in situ genome-wide profiling with high efficiency for low cell numbers
- (2018) Peter J Skene et al. Nature Protocols
- Patterns of chromatin accessibility along the anterior-posterior axis in the early Drosophila embryo
- (2018) Jenna E. Haines et al. PLoS Genetics
- Computational Methods for Assessing Chromatin Hierarchy
- (2018) Pearl Chang et al. Computational and Structural Biotechnology Journal
- Principles of nucleosome organization revealed by single-cell micrococcal nuclease sequencing
- (2018) Binbin Lai et al. NATURE
- Chromatin accessibility landscape of articular knee cartilage reveals aberrant enhancer regulation in osteoarthritis
- (2018) Ye Liu et al. Scientific Reports
- A chromatin integration labelling method enables epigenomic profiling with lower input
- (2018) Akihito Harada et al. NATURE CELL BIOLOGY
- The chromatin accessibility landscape of primary human cancers
- (2018) M. Ryan Corces et al. SCIENCE
- Chromatin accessibility dynamics reveal novel functional enhancers inC. elegans
- (2017) Aaron C. Daugherty et al. GENOME RESEARCH
- Impact of regulatory variation across human iPSCs and differentiated cells
- (2017) Nicholas E. Banovich et al. GENOME RESEARCH
- Inflammatory memory sensitizes skin epithelial stem cells to tissue damage
- (2017) Shruti Naik et al. NATURE
- Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements
- (2017) Maxwell R Mumbach et al. NATURE GENETICS
- chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data
- (2017) Alicia N Schep et al. NATURE METHODS
- An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues
- (2017) M Ryan Corces et al. NATURE METHODS
- Understanding nucleosome dynamics and their links to gene expression and DNA replication
- (2017) William K. M. Lai et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
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- (2017) André L Martins et al. NUCLEIC ACIDS RESEARCH
- JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework
- (2017) Aziz Khan et al. NUCLEIC ACIDS RESEARCH
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- (2017) Orly L. Wapinski et al. Cell Reports
- An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites
- (2017) Peter J Skene et al. eLife
- TFBSTools: an R/bioconductor package for transcription factor binding site analysis
- (2016) Ge Tan et al. BIOINFORMATICS
- Nfib Promotes Metastasis through a Widespread Increase in Chromatin Accessibility
- (2016) Sarah K. Denny et al. CELL
- The Spectrum and Regulatory Landscape of Intestinal Innate Lymphoid Cells Are Shaped by the Microbiome
- (2016) Meital Gury-BenAri et al. CELL
- The landscape of accessible chromatin in mammalian preimplantation embryos
- (2016) Jingyi Wu et al. NATURE
- Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution
- (2016) M Ryan Corces et al. NATURE GENETICS
- Genome-wide footprinting: ready for prime time?
- (2016) Myong-Hee Sung et al. NATURE METHODS
- ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing
- (2016) Xingqi Chen et al. NATURE METHODS
- HiChIP: efficient and sensitive analysis of protein-directed genome architecture
- (2016) Maxwell R Mumbach et al. NATURE METHODS
- MNase titration reveals differences between nucleosome occupancy and chromatin accessibility
- (2016) Jakub Mieczkowski et al. Nature Communications
- ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization
- (2015) Guangchuang Yu et al. BIOINFORMATICS
- Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions
- (2015) Alicia N. Schep et al. GENOME RESEARCH
- Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples
- (2015) Wenfei Jin et al. NATURE
- Single-cell chromatin accessibility reveals principles of regulatory variation
- (2015) Jason D. Buenrostro et al. NATURE
- Fine-mapping cellular QTLs with RASQUAL and ATAC-seq
- (2015) Natsuhiko Kumasaka et al. NATURE GENETICS
- ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors
- (2015) Christian Schmidl et al. NATURE METHODS
- Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain
- (2015) Alisa Mo et al. NEURON
- limma powers differential expression analyses for RNA-sequencing and microarray studies
- (2015) Matthew E. Ritchie et al. NUCLEIC ACIDS RESEARCH
- Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing
- (2015) D. A. Cusanovich et al. SCIENCE
- SAMBLASTER: fast duplicate marking and structural variant read extraction
- (2014) G. G. Faust et al. BIOINFORMATICS
- Trimmomatic: a flexible trimmer for Illumina sequence data
- (2014) Anthony M. Bolger et al. BIOINFORMATICS
- Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads
- (2014) Hongshan Jiang et al. BMC BIOINFORMATICS
- Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity
- (2014) Matthew T. Weirauch et al. CELL
- Tn5 transposase and tagmentation procedures for massively scaled sequencing projects
- (2014) Simone Picelli et al. GENOME RESEARCH
- Normalization of RNA-seq data using factor analysis of control genes or samples
- (2014) Davide Risso et al. NATURE BIOTECHNOLOGY
- Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification
- (2013) Housheng Hansen He et al. NATURE METHODS
- Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
- (2013) Jason D Buenrostro et al. NATURE METHODS
- Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments
- (2013) P. Kheradpour et al. NUCLEIC ACIDS RESEARCH
- Chromatin Accessibility Data Sets Show Bias Due to Sequence Specificity of the DNase I Enzyme
- (2013) Hashem Koohy et al. PLoS One
- Probing DNA shape and methylation state on a genomic scale with DNase I
- (2013) A. Lazarovici et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Cell-type-specific nuclei purification from whole animals for genome-wide expression and chromatin profiling
- (2012) F. A. Steiner et al. GENOME RESEARCH
- Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules
- (2012) T. K. Kelly et al. GENOME RESEARCH
- Hi–C: A comprehensive technique to capture the conformation of genomes
- (2012) Jon-Matthew Belton et al. METHODS
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions
- (2012) Terrence S. Furey NATURE REVIEWS GENETICS
- Insertion site preference of Mu, Tn5, and Tn7 transposons
- (2012) Brian Green et al. Mobile DNA
- Mapping and analysis of chromatin state dynamics in nine human cell types
- (2011) Jason Ernst et al. NATURE
- Integrative genomics viewer
- (2011) James T Robinson et al. NATURE BIOTECHNOLOGY
- BEDTools: a flexible suite of utilities for comparing genomic features
- (2010) Aaron R. Quinlan et al. BIOINFORMATICS
- ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
- (2010) Lihua J Zhu et al. BMC BIOINFORMATICS
- A Simple Method for Gene Expression and Chromatin Profiling of Individual Cell Types within a Tissue
- (2010) Roger B. Deal et al. DEVELOPMENTAL CELL
- Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
- (2010) Sven Heinz et al. MOLECULAR CELL
- Discovery and characterization of chromatin states for systematic annotation of the human genome
- (2010) Jason Ernst et al. NATURE BIOTECHNOLOGY
- The INTACT method for cell type–specific gene expression and chromatin profiling in Arabidopsis thaliana
- (2010) Roger B Deal et al. Nature Protocols
- DNA transposon Hermes inserts into DNA in nucleosome-free regions in vivo
- (2010) S. Gangadharan et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition
- (2010) Andrew Adey et al. GENOME BIOLOGY
- Fast and accurate short read alignment with Burrows-Wheeler transform
- (2009) H. Li et al. BIOINFORMATICS
- edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
- (2009) M. D. Robinson et al. BIOINFORMATICS
- Global mapping of protein-DNA interactions in vivo by digital genomic footprinting
- (2009) Jay R Hesselberth et al. NATURE METHODS
- MEME SUITE: tools for motif discovery and searching
- (2009) T. L. Bailey et al. NUCLEIC ACIDS RESEARCH
- F-Seq: a feature density estimator for high-throughput sequence tags
- (2008) A. P. Boyle et al. BIOINFORMATICS
- Dynamic Regulation of Nucleosome Positioning in the Human Genome
- (2008) Dustin E. Schones et al. CELL
- High-Resolution Mapping and Characterization of Open Chromatin across the Genome
- (2008) Alan P. Boyle et al. CELL
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