Data from: DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci

This dataset contains the raw sequencing data, processed alignments,
fluorescent microscopy images, and tabular figure source data associated
with the development and application of DNA O-MAP, a method for profiling
the proteins and DNA interactions proximal to specific genomic loci in
fixed cells. The dataset includes: (1) 14 paired-end FASTQ files from
Illumina MiSeq sequencing of DNA O-MAP experiments targeting single-copy
chromatin loop anchors on chromosomes 3, 10, and 19 in HCT 116 cells; (2)
10 BAM alignment files (GRCh38/hg38, ENCODE blacklist-filtered) derived
from these sequencing libraries; (3) 20 raw three-dimensional fluorescent
microscopy image stacks (.nd2 format) used to quantify labeling
specificity and efficiency for telomere, pericentromeric alpha-satellite,
mitochondrial, and no-probe control conditions; (4) 48 individual
micrograph panels (PNG) used in manuscript figures; and (5) 32 CSV files
and 1 Cytoscape JSON file containing the processed numerical data
underlying all manuscript figure panels, including proteomic enrichment
analyses, gene set enrichment results, genome coverage profiles, and
protein interaction networks. FASTQ and BAM files can be reanalyzed with
standard genomic alignment tools. Microscopy files can be opened with
Fiji/ImageJ (Bio-Formats plugin) or NIS-Elements. Tabular data files can
be read with R, Python, or any spreadsheet software.