Results 11 to 20 of about 176,761 (289)
, 2022 ATAC-seq BED files for HepG2, HEK293, and LoVo cell lines used in ...
TAREIAN A CAZARES
core +5 more sources
Identification of transcription factor binding sites using ATAC-seq [PDF]
Genome Biology, 2019 Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) is a simple protocol for detection of open chromatin. Computational footprinting, the search for regions with depletion of cleavage events due to transcription factor binding, is poorly ...
Zhijian Li +5 more
doaj +5 more sources
Successful ATAC-Seq From Snap-Frozen Equine Tissues [PDF]
Frontiers in Genetics, 2021 An assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) has become an increasingly popular method to assess genome-wide chromatin accessibility in isolated nuclei from fresh tissues.
Sichong Peng +5 more
doaj +2 more sources
A simple ATAC-seq protocol for population epigenetics [PDF]
Wellcome Open Research, 2021 We describe here a protocol for the generation of sequence-ready libraries for population epigenomics studies, and the analysis of alignment results. We show that the protocol can be used to monitor chromatin structure changes in populations when exposed to environmental cues.
Augusto, Ronaldo de Carvalho +20 more
openaire +5 more sources
Chromatin accessibility profiling by ATAC-seq
Nature Protocols, 2022 The assay for transposase-accessible chromatin using sequencing (ATAC-seq) provides a simple and scalable way to detect the unique chromatin landscape associated with a cell type and how it may be altered by perturbation or disease. ATAC-seq requires a relatively small number of input cells and does not require a priori knowledge of the epigenetic ...
Grandi, Fiorella +3 more
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Unsupervised contrastive peak caller for ATAC-seq
Genome Research, 2023 The assay for transposase-accessible chromatin with sequencing (ATAC-seq) is a common assay to identify chromatin accessible regions by using a Tn5 transposase that can access, cut, and ligate adapters to DNA fragments for subsequent amplification and sequencing.
Ha T.H. Vu +3 more
openaire +3 more sources
ATAC-seq-specific normalization is required to for robust prediction across ATAC-seq protocols.
, 2023 (A) Max RP20M value per autosomal chromosome before and after filtering extended blacklist regions. (B) An example tandem repeat region with variable signal found on Chr17.
Anthony T. Bejjani (14526729) +14 more
core +1 more source
ENCODE-DCC/atac-seq-pipeline: v2.2.0
, 2022 Upgrade Caper to >=2.2.0 for new HPC features. $ pip install caper>=2.2.0 --upgrade Conda environment name change: encode-atac-seq-pipeline -> encd-atac Please reinstall your Conda environment after updating pipeline's git repo.
Jin wook Lee +7 more
core +1 more source
STAR Protocols, 2021 Summary: ATAC-seq is a versatile, adaptable, and widely adopted technique for mapping open chromatin regions. However, some biological systems, such as primary neurons, present unique challenges to its application. Conventional ATAC-seq would require the
Maya Maor-Nof +4 more
doaj +1 more source