scholarly journals Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing

2013 ◽  
Vol 10 (4) ◽  
pp. 361-365 ◽  
Author(s):  
Nicola Crosetto ◽  
Abhishek Mitra ◽  
Maria Joao Silva ◽  
Magda Bienko ◽  
Norbert Dojer ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Strand Break ◽  
Double Strand Break ◽  
Next Generation ◽  
Dna Double Strand Break ◽  
Nucleotide Resolution ◽  
Generation Sequencing

scholarly journals BAMscale: quantification of next-generation sequencing peaks and generation of scaled coverage tracks

2020 ◽  
Author(s):  
Lorinc Pongor ◽  
Jacob M Gross ◽  
Roberto Vera Alvarez ◽  
Junko Murai ◽  
Sang-Min Jang ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Replication Timing ◽  
Strand Break ◽  
Computational Time ◽  
Rna Seq ◽  
Next Generation ◽  
Dna Double Strand Break ◽  
Chromatin Immunoprecipitation Sequencing ◽  
One Step ◽  
Generation Sequencing

Abstract Background: Next-generation sequencing allows genome-wide analysis of changes in chromatin states and gene expression. Data analysis of these increasingly used methods either requires multiple analysis steps, or extensive computational time. We sought to develop a tool for rapid quantification of sequencing peaks, and an efficient method to produce coverage tracks for accurate visualization that can be intuitively interpreted by experimentalists with minimal bioinformatics background. We demonstrate its strength by integrating data from several types of sequencing approaches. Results: We have developed BAMscale, a one-step tool that processes a wide set of sequencing datasets. To demonstrate the usefulness of BAMscale, we analyzed multiple sequencing datasets from chromatin immunoprecipitation sequencing (ChIP-seq) data, chromatin state change data (Assay for Transposase-Accessible Chromatin using sequencing: ATAC-seq, DNA double strand break mapping sequencing: END-seq), DNA replication data (Okazaki fragments sequencing: OK-seq, Nascent-strand sequencing: NS-seq, single-cell replication timing sequencing: scRepli-seq) and RNA-seq data. The outputs consist of raw and normalized peak scores (multiple normalizations) in text format and scaled bigWig coverage tracks that are directly accessible to data visualization programs. Our tool can effectively analyze large sequencing datasets (~100Gb size) in minutes, outperforming currently available tools.Conclusions: BAMscale is a tool that can be used to accurately quantify and normalize identified peaks directly from BAM files, as well as create coverage tracks for visualization in genome browsers. BAMScale can be implemented for a wide set of methods for calculating coverage tracks such as ChIP-seq / ATAC-seq, as well as splice aware RNA-seq, END-seq and OK-seq for which no dedicated software is available. BAMscale is freely available on github (https://github.com/ncbi/BAMscale).

Development of a novel method to create double-strand break repair fingerprints using next-generation sequencing

DNA Repair ◽  
2015 ◽  
Vol 26 ◽  
pp. 44-53 ◽  
Author(s):  
Chen-Pang Soong ◽  
Gregory A. Breuer ◽  
Ryan A. Hannon ◽  
Savina D. Kim ◽  
Ahmed F. Salem ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Strand Break ◽  
Double Strand Break ◽  
Double Strand Break Repair ◽  
Next Generation ◽  
Novel Method ◽  
Break Repair ◽  
Generation Sequencing

scholarly journals BAMscale: quantification of next-generation sequencing peaks and generation of scaled coverage tracks

2020 ◽  
Author(s):  
Lorinc Pongor ◽  
Jacob M Gross ◽  
Roberto Vera Alvarez ◽  
Junko Murai ◽  
Sang-Min Jang ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Replication Timing ◽  
Strand Break ◽  
Computational Time ◽  
Rna Seq ◽  
Next Generation ◽  
Sequencing Data ◽  
Dna Double Strand Break ◽  
Chromatin Immunoprecipitation Sequencing ◽  
Generation Sequencing

Abstract Background Next-generation sequencing allows genome-wide analysis of changes in chromatin states and gene expression. Data analysis of these increasingly used methods either requires multiple analysis steps, or extensive computational time. We sought to develop a tool for rapid quantification of sequencing peaks from diverse experimental sources and an efficient method to produce coverage tracks for accurate visualization that can be intuitively displayed and interpreted by experimentalists with minimal bioinformatics background. We demonstrate its strength and usability by integrating data from several types of sequencing approaches. Results We have developed BAMscale , a one-step tool that processes a wide set of sequencing datasets. To demonstrate the usefulness of BAMscale , we analyzed multiple sequencing datasets from chromatin immunoprecipitation sequencing data (ChIP-seq), chromatin state change data (Assay for Transposase-Accessible Chromatin using sequencing: ATAC-seq, DNA double-strand break mapping sequencing: END-seq), DNA replication data (Okazaki fragments sequencing: OK-seq, Nascent-strand sequencing: NS-seq, single-cell replication timing sequencing: scRepli-seq) and RNA-seq data. The outputs consist of raw and normalized peak scores (multiple normalizations) in text format and scaled bigWig coverage tracks that are directly accessible to data visualization programs. BAMScale also includes a visualization module facilitating direct, on-demand quantitative peak comparisons that can be used by experimentalists. Our tool can effectively analyze large sequencing datasets (~100Gb size) in minutes, outperforming currently available tools. Conclusions BAMscale accurately quantifies and normalizes identified peaks directly from BAM files, and creates coverage tracks for visualization in genome browsers. BAMScale can be implemented for a wide set of methods for calculating coverage tracks, including ChIP-seq and ATAC-seq, as well as methods that currently require specialized, separate tools for analyses, such as splice aware RNA-seq, END-seq and OK-seq for which no dedicated software is available. BAMscale is freely available on github ( https://github.com/ncbi/BAMscale ).

scholarly journals Mapping DNA Topoisomerase Binding and Cleavage Genome Wide Using Next-Generation Sequencing Techniques

Genes ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 92 ◽  
Author(s):  
Shannon J. McKie ◽  
Anthony Maxwell ◽  
Keir C. Neuman
Keyword(s):  
Next Generation Sequencing ◽  
Dna Cleavage ◽  
Next Generation ◽  
Dna Breaks ◽  
Genome Wide ◽  
Extension Activity ◽  
Nucleotide Resolution ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Next-generation sequencing (NGS) platforms have been adapted to generate genome-wide maps and sequence context of binding and cleavage of DNA topoisomerases (topos). Continuous refinements of these techniques have resulted in the acquisition of data with unprecedented depth and resolution, which has shed new light on in vivo topo behavior. Topos regulate DNA topology through the formation of reversible single- or double-stranded DNA breaks. Topo activity is critical for DNA metabolism in general, and in particular to support transcription and replication. However, the binding and activity of topos over the genome in vivo was difficult to study until the advent of NGS. Over and above traditional chromatin immunoprecipitation (ChIP)-seq approaches that probe protein binding, the unique formation of covalent protein–DNA linkages associated with DNA cleavage by topos affords the ability to probe cleavage and, by extension, activity over the genome. NGS platforms have facilitated genome-wide studies mapping the behavior of topos in vivo, how the behavior varies among species and how inhibitors affect cleavage. Many NGS approaches achieve nucleotide resolution of topo binding and cleavage sites, imparting an extent of information not previously attainable. We review the development of NGS approaches to probe topo interactions over the genome in vivo and highlight general conclusions and quandaries that have arisen from this rapidly advancing field of topoisomerase research.

DSBCapture: in situ single-nucleotide resolution DNA double-strand break mapping

2016 ◽  
Author(s):  
Stefanie Lensing ◽  
Stefanie Lensing ◽  
Giovanni Marsico ◽  
Robert Hänsel-Hertsch ◽  
Enid Lam ◽  
...  
Keyword(s):  
Strand Break ◽  
Double Strand Break ◽  
Single Nucleotide ◽  
Dna Double Strand Break ◽  
Nucleotide Resolution ◽  
Single Nucleotide Resolution
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