Results 51 to 60 of about 186,580 (246)

ATAC-Seq of a Single Myofiber from Mus musculus

BIO-PROTOCOL, 2022
Chromatin accessibility is a key determinant of gene expression that can be altered under different physiological and disease conditions. Skeletal muscle is made up of myofibers that are highly plastic and adaptive. Therefore, assessing the genome-wide chromatin state of myofibers under various conditions is very important to gain insight into the ...
Korin Sahinyan, Darren Blackburn, Vahab Soleimani   +2 more
openaire   +3 more sources

Chromatin-accessibility estimation from single-cell ATAC-seq data with scOpen

Nature Communications, 2021
A major drawback of single-cell ATAC-seq (scATAC-seq) is its sparsity, i.e., open chromatin regions with no reads due to loss of DNA material during the scATAC-seq protocol.
Zhijian Li, C. Kuppe, S. Ziegler, Mingbo Cheng, Nazanin Kabgani, Sylvia Menzel, M. Zenke, R. Kramann, I. Costa   +8 more
semanticscholar   +1 more source

Low-input ATAC&mRNA-seq protocol for simultaneous profiling of chromatin accessibility and gene expression

STAR Protocols, 2021
Summary: We present a simple, fast, and robust protocol (low-input ATAC&mRNA-seq) to simultaneously generate ATAC-seq and mRNA-seq libraries from the same cells in limited cell numbers by coupling a simplified ATAC procedure using whole cells with a ...
Ruifang Li, Sara A. Grimm, Paul A. Wade
doaj   +1 more source

An ATAC-seq atlas of chromatin accessibility in mouse tissues [PDF]

Scientific Data, 2019
Abstract The Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is a fundamental epigenomics approach and has been widely used in profiling the chromatin accessibility dynamics in multiple species. A comprehensive reference of ATAC-seq datasets for mammalian tissues is important for the understanding of regulatory ...
Liu, Chuanyu, Wang, Mingyue, Wei, Xiaoyu, Wu, Liang, Xu, Jiangshan, Dai, Xi, Xia, Jun, Cheng, Mengnan, Yuan, Yue, Zhang, Pengfan, Li, Jiguang, Feng, Taiqing, Chen, Ao, Zhang, Wenwei, Chen, Fang, Shang, Zhouchun, Zhang, Xiuqing, Peters, Brock A., Liu, Longqi   +18 more
openaire   +3 more sources

Beyond accessibility: ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation

bioRxiv, 2019
While footprinting analysis of ATAC-seq data can theoretically enable investigation of transcription factor (TF) binding, the lack of a computational tool able to conduct different levels of footprinting analysis has so-far hindered the widespread ...
Mette Bentsen, Philipp Goymann, H. Schultheis, K. Klee, Anastasiia Petrova, R. Wiegandt, A. Fust, J. Preussner, C. Kuenne, T. Braun, Johnny Kim, M. Looso   +11 more
semanticscholar   +1 more source

HMMRATAC: a Hidden Markov ModeleR for ATAC-seq

Nucleic Acids Research, 2018
ABSTRACT ATAC-seq has been widely adopted to identify accessible chromatin regions across the genome. However, current data analysis still utilizes approaches initially designed for ChIP-seq or DNase-seq, without considering the transposase digested DNA fragments that contain additional nucleosome positioning information. We present the
Tarbell, Evan D., Liu, Tao
openaire   +2 more sources

Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets using protocol-specific bias modeling

Genome Biology, 2019
Background DNase-seq and ATAC-seq are broadly used methods to assay open chromatin regions genome-wide. The single nucleotide resolution of DNase-seq has been further exploited to infer transcription factor binding sites (TFBSs) in regulatory regions ...
Aslıhan Karabacak Calviello, Antje Hirsekorn, Ricardo Wurmus, Dilmurat Yusuf, Uwe Ohler   +4 more
doaj   +1 more source

Protocol for assay of transposase accessible chromatin sequencing in non-model species

STAR Protocols, 2021
Summary: The assay for transposase accessible chromatin (ATAC-seq) is a method for mapping genome-wide chromatin accessibility. Coupled with high-throughput sequencing, it enables integrative epigenomics analyses.
Stephen Kissane, Vignesh Dhandapani, Luisa Orsini   +2 more
doaj   +1 more source

Uniform quantification of single-nucleus ATAC-seq data with Paired-Insertion Counting (PIC) and a model-based insertion rate estimator

Nature Methods, 2023
Existing approaches to scoring single-nucleus assay for transposase-accessible chromatin with sequencing (snATAC-seq) feature matrices from sequencing reads are inconsistent, affecting downstream analyses and displaying artifacts. We show that, even with
Zhen Miao, Junhyong Kim
semanticscholar   +1 more source

Fine-mapping cellular QTLs with RASQUAL and ATAC-seq [PDF]

Nature Genetics, 2015
Abstract When cellular traits are measured using high-throughput DNA sequencing quantitative trait loci (QTLs) manifest at two levels: population level differences between individuals and allelic differences between cis -haplotypes within individuals.
Kumasaka, Natsuhiko, Knights, Andrew, Gaffney, Daniel   +2 more
openaire   +3 more sources