Results 51 to 60 of about 176,761 (289)
ATAC-seq and NFKB1 ChIP-seq peak pairwise normalized read count comparisons.
, 2022 Each dot represents a peak that is present in either of the two samples. The X- and Y-axis indicate the number of normalized read counts for that peak in the two samples.
Daniel Miller (424185) +18 more
core +1 more source
From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis
Genome Biology, 2020 Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) is widely used in studying chromatin biology, but a comprehensive review of the analysis tools has not been completed yet.
Feng Yan +3 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 +2 more
doaj +1 more source
, 2020 (A) Volcano plot to show differentially accessible peaks, nominally significant peaks (p = 0.05) and shown in pink. (B) Annotation of an example peaks shows increased counts at transcription start sites.
Stephanie Bien (3219345) +6 more
core +1 more source
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 +4 more
doaj +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
ATAC-seq footprints of different promoter classes.
, 2021 Single-base resolution ATAC-seq footprints are shown for the three most prominent promoter classes (Figs 2 and 3) in Drosophila (A) and Homo sapiens (B).
Diana Ideses (1805743) +5 more
core +1 more source
Epigenetics & Chromatin, 2020 Background Chromatin dysregulation is associated with developmental disorders and cancer. Numerous methods for measuring genome-wide chromatin accessibility have been developed in the genomic era to interrogate the function of chromatin regulators.
Jake J. Reske +2 more
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 +18 more
openaire +3 more sources
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 +2 more
openaire +3 more sources