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CAM: A quality control pipeline for MNase-seq data.

Sheng'en Hu1, Xiaolan Chen1, Ji Liao1

  • 1Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Science and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai, China.

Plos One
|August 9, 2017
PubMed
Summary
This summary is machine-generated.

We developed CAM, a quality control pipeline for Micrococcal nuclease digestion followed by high-throughput sequencing (MNase-seq) data. CAM ensures accurate nucleosome organization analysis and provides a reference atlas for unbiased assessment.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Nucleosome organization is crucial for regulating gene accessibility.
  • Micrococcal nuclease digestion followed by high-throughput sequencing (MNase-seq) is a primary method for genome-wide nucleosome profiling.
  • Assessing MNase-seq data quality, particularly in mammals, presents significant challenges.

Purpose of the Study:

  • To develop a comprehensive and user-friendly quality control (QC) pipeline for MNase-seq data analysis.
  • To provide standardized QC measurements and nucleosome organization profiles.
  • To establish a reference atlas for unbiased data assessment.

Main Methods:

  • Development of the CAM (Comprehensive Assessment of MNase-seq) pipeline.
  • Implementation of multiple informative QC metrics within CAM.
  • Inclusion of a reference atlas comprising 268 historical human and mouse MNase-seq datasets.

Main Results:

  • CAM offers a robust framework for evaluating MNase-seq data quality.
  • The pipeline generates detailed nucleosome organization profiles across functional genomic regions.
  • A comprehensive reference atlas enables unbiased comparison and assessment of new datasets.

Conclusions:

  • CAM addresses the need for a convenient and comprehensive QC approach for MNase-seq data.
  • The pipeline facilitates more reliable analysis of nucleosome organization.
  • CAM enhances the accuracy and interpretability of MNase-seq studies in mammalian systems.