plot2DO

plot2DO visualizes two-dimensional occupancy of sequencing fragments to assess nucleosome positioning and chromatin organization from MNase-seq, MNase-ChIP-seq, ChIP-seq, ATAC-seq, and chemical cleavage mapping data.

Key Features:

• Data Quality Evaluation: Assesses MNase-seq data quality to support accurate genome-wide interpretation of nucleosome positioning and chromatin structure.
• Visualization Capabilities: Produces 2D occupancy plots that display nucleosome distribution relative to functional genomic regions.
• Flexibility Across Data Types: Applies to MNase-seq, MNase-ChIP-seq, ChIP-seq, ATAC-seq, and chemical cleavage mapping to analyze DNA fragment distribution across genomic regions.

Scientific Applications:

• Chromatin organization and epigenetic regulation: Provides occupancy and fragment-size information to study nucleosome arrangement and chromatin accessibility.
• Stem cell pluripotency and differentiation: Enables analysis of chromatin structure changes that influence gene expression during pluripotency and differentiation.
• Histone modification and variant distribution analysis: Integrates with ChIP-seq data for high-resolution investigation of histone modifications and variant distributions.

Methodology:

Analyzes DNA fragments generated by MNase digestion followed by sequencing by evaluating fragment size distribution and occupancy across genomic regions to infer nucleosome positioning and chromatin accessibility.