Articles with "atac seq" as a keyword



Photo by nci from unsplash

Epigenomic features revealed by ATAC‐seq impact transgene expression in CHO cells

Sign Up to like & get
recommendations!
Published in 2021 at "Biotechnology and Bioengineering"

DOI: 10.1002/bit.27701

Abstract: Different regions of a mammalian genome have different accessibilities to transcriptional machinery. The integration site of a transgene affects how actively it is transcribed. Highly accessible genomic regions called super‐enhancers have been recently described as… read more here.

Keywords: integration; atac seq; cho cells; super enhancer ... See more keywords
Photo from wikipedia

RNA‐seq and ATAC‐seq analyses of multilineage differentiating stress enduring cells: Comparison with dermal fibroblasts

Sign Up to like & get
recommendations!
Published in 2022 at "Cell Biology International"

DOI: 10.1002/cbin.11834

Abstract: The aim of this study is to characterize the molecular properties of multilineage differentiating stress‐enduring (Muse) cells compared with dermal fibroblasts (FBs) and to characterize differences in their transcriptomes and open chromatin regions that are… read more here.

Keywords: muse cells; atac seq; seq; seq analyses ... See more keywords
Photo from archive.org

Interrogating the Accessible Chromatin Landscape of Eukaryote Genomes Using ATAC-seq.

Sign Up to like & get
recommendations!
Published in 2021 at "Methods in molecular biology"

DOI: 10.1007/978-1-0716-1103-6_10

Abstract: The ATAC-seq assay has emerged as the most useful, versatile, and widely adaptable method for profiling accessible chromatin regions and tracking the activity of cis-regulatory elements (cREs) in eukaryotes. Thanks to its great utility, it… read more here.

Keywords: accessible chromatin; atac seq; chromatin; interrogating accessible ... See more keywords
Photo by jakubpabis from unsplash

Assay for Transposase Accessible Chromatin (ATAC-Seq) to Chart the Open Chromatin Landscape of Human Pancreatic Islets.

Sign Up to like & get
recommendations!
Published in 2018 at "Methods in molecular biology"

DOI: 10.1007/978-1-4939-7768-0_11

Abstract: The regulatory mechanisms that ensure an accurate control of gene transcription are central to cellular function, development and disease. Such mechanisms rely largely on noncoding regulatory sequences that allow the establishment and maintenance of cell… read more here.

Keywords: transposase accessible; accessible chromatin; atac seq; chromatin ... See more keywords
Photo by campaign_creators from unsplash

Quantification, Dynamic Visualization, and Validation of Bias in ATAC-Seq Data with ataqv.

Sign Up to like & get
recommendations!
Published in 2020 at "Cell systems"

DOI: 10.1016/j.cels.2020.02.009

Abstract: The assay for transposase-accessible chromatin using sequencing (ATAC-seq) has become the preferred method for mapping chromatin accessibility due to its time and input material efficiency. However, it can be difficult to evaluate data quality and identify… read more here.

Keywords: atac seq; seq data; bias; bias atac ... See more keywords
Photo from wikipedia

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

Sign Up to like & get
recommendations!
Published in 2020 at "Nature Communications"

DOI: 10.1038/s41467-020-18035-1

Abstract: 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 application… read more here.

Keywords: transcription factor; factor binding; zygotic genome; atac seq ... See more keywords
Photo by nci from unsplash

Transcript-indexed ATAC-seq for precision immune profiling

Sign Up to like & get
recommendations!
Published in 2018 at "Nature medicine"

DOI: 10.1038/s41591-018-0008-8

Abstract: T cells create vast amounts of diversity in the genes that encode their T cell receptors (TCRs), which enables individual clones to recognize specific peptide–major histocompatibility complex (MHC) ligands. Here we combined sequencing of the… read more here.

Keywords: leukemic cells; atac seq; transcript indexed; indexed atac ... See more keywords
Photo by kellysikkema from unsplash

Reducing mitochondrial reads in ATAC-seq using CRISPR/Cas9

Sign Up to like & get
recommendations!
Published in 2017 at "Scientific Reports"

DOI: 10.1038/s41598-017-02547-w

Abstract: ATAC-seq is a high-throughput sequencing technique that identifies open chromatin. Depending on the cell type, ATAC-seq samples may contain ~20–80% of mitochondrial sequencing reads. As the regions of open chromatin of interest are usually located… read more here.

Keywords: number; mitochondrial reads; using crispr; atac seq ... See more keywords
Photo by goumbik from unsplash

MMGraph: a multiple motif predictor based on graph neural network and coexisting probability for ATAC-seq data

Sign Up to like & get
recommendations!
Published in 2022 at "Bioinformatics"

DOI: 10.1093/bioinformatics/btac572

Abstract: Abstract Motivation Transcription factor binding sites (TFBSs) prediction is a crucial step in revealing functions of transcription factors from high-throughput sequencing data. Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) provides insight on TFBSs and nucleosome… read more here.

Keywords: graph neural; seq data; neural network; atac seq ... See more keywords
Photo by michael75 from unsplash

Genetic variation in chromatin state across multiple tissues in Drosophila melanogaster

Sign Up to like & get
recommendations!
Published in 2022 at "PLOS Genetics"

DOI: 10.1101/2022.09.26.509449

Abstract: We use ATAC-seq to examine chromatin accessibility for four different tissues in Drosophila melanogaster: adult female brain, ovaries, and both wing and eye-antennal imaginal discs from males. Each tissue is assayed in eight different inbred… read more here.

Keywords: atac seq; chromatin state; chromatin; tissues drosophila ... See more keywords
Photo by wulcan from unsplash

ATAC-Seq Reveals an Isl1 Enhancer That Regulates Sinoatrial Node Development and Function

Sign Up to like & get
recommendations!
Published in 2020 at "Circulation Research"

DOI: 10.1161/circresaha.120.317145

Abstract: Supplemental Digital Content is available in the text. Rationale: Cardiac pacemaker cells (PCs) in the sinoatrial node (SAN) have a distinct gene expression program that allows them to fire automatically and initiate the heartbeat. Although… read more here.

Keywords: sinoatrial node; atac seq; development; gene ... See more keywords