Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets using protocol-specific bias modeling [PDF]
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 ...
Antje Hirsekorn, Uwe Ohler, Ohler Uwe
exaly +4 more sources
A Comparison of Peak Callers Used for DNase-Seq Data [PDF]
PLoS ONE, 2014 Genome-wide profiling of open chromatin regions using DNase I and high-throughput sequencing (DNase-seq) is an increasingly popular approach for finding and studying regulatory elements.
Hashem Koohy +2 more
exaly +4 more sources
Comparative evaluation of DNase-seq footprint identification strategies [PDF]
Frontiers in Genetics, 2014 DNase I is an enzyme preferentially cleaving DNA in highly accessible regions. Recently, Next-Generation Sequencing has been applied to DNase I assays (DNase-seq) to obtain genome-wide maps of these accessible chromatin regions.With high-depth sequencing,
Iros Barozzi +2 more
exaly +4 more sources
XL-DNase-seq: improved footprinting of dynamic transcription factors [PDF]
Epigenetics & Chromatin, 2019 Background As the cost of high-throughput sequencing technologies decreases, genome-wide chromatin accessibility profiling methods such as the assay of transposase-accessible chromatin using sequencing (ATAC-seq) are employed widely, with data ...
Kyu-Seon Oh +3 more
doaj +2 more sources
Which Genetics Variants in DNase-Seq Footprints Are More Likely to Alter Binding? [PDF]
PLoS Genetics, 2016 Large experimental efforts are characterizing the regulatory genome, yet we are still missing a systematic definition of functional and silent genetic variants in non-coding regions.
Gregory A Moyerbrailean +5 more
doaj +2 more sources
Practical NicE-seq workflow for chromatin accessibility analysis in plants [PDF]
Molecules and Cells: Open chromatin profiling identifies regulatory DNA regions that are accessible to transcription factors and other proteins, offering insights into gene regulation.
Zein Eddin Bader +4 more
doaj +2 more sources
Corrigendum: Comparative evaluation of DNase-seq footprint identification strategies [PDF]
Frontiers in Genetics, 2014 Iros eBarozzi +2 more
doaj +2 more sources
Chromatin accessibility landscape of stromal subpopulations reveals distinct metabolic and inflammatory features of porcine subcutaneous and visceral adipose tissue [PDF]
PeerJ, 2022 Background Fat accumulation in visceral adipose tissue (VAT) confers increased risk for metabolic disorders of obesity, whereas accumulation of subcutaneous adipose tissue (SAT) is associated with lower risk and may be protective.
Wenyang Sun +7 more
doaj +2 more sources
Romulus: robust multi-state identification of transcription factor binding sites from DNase-seq data [PDF]
Bioinformatics, 2016 Aleksander Jankowski +2 more
exaly +2 more sources
Prediction accuracy of regulatory elements from sequence varies by functional sequencing technique
Frontiers in Cellular and Infection Microbiology, 2023 IntroductionVarious sequencing based approaches are used to identify and characterize the activities of cis-regulatory elements in a genome-wide fashion.
Ronald J. Nowling +3 more
doaj +1 more source