README file for the Nott_2019_PLAC-seq_hg19 dataset I. Description of the dataset -------------------------------- Data source: Nott_2019 Data source URL: http://homer.ucsd.edu/iholtman/Nuclei_project/interaction/MAPS/ Genome build: hg19 File format: bed bed4+19 interact, bgzip-compressed and tabix-indexed Contents: PLAC-seq H3K4me3 chromatin interactions Dataset URL: https://tf.lisanwanglab.org/GADB/FILER2/Annotationtracks/Nott_2019/PLAC-seq/bed4plus19_interact/hg19/ Acknowledgements: https://tf.lisanwanglab.org/GADB/FILER2/acknowledgements/Nott_2019.html II. Dataset version number -------------------------------- v2_0529_2026 III. Files in the dataset -------------------------------- See MANIFEST for the complete file list. Summary: - Files: 3 *.bed.gz files - Auxiliary indexes: giggle_index/ IV. Contributors -------------------------------- Jeffrey Cifello Prabhakaran Gangadharan Luke Carter Pavel P. Kuksa Fanny Leung V. Workflow description -------------------------------- Files were processed and standardized using FILER data integration and harmonization pipeline (hipFG). VI. Input files and Resources -------------------------------- Original files were obtained from http://homer.ucsd.edu/iholtman/Nuclei_project/interaction/MAPS/. VII. File Contents -------------------------------- 1. Example annotation file: formatted_output_Microglia_PLAC_seq.bed.gz File schema: fieldName sqlType fieldDescription anchorChrom string Chromosome of the anchor region anchorStart uint Start position of the anchor region anchorEnd uint End position of the anchor region anchorName string Identifier for the anchor interactionAttr string Interaction attributes for source and target genes chrom string Reference sequence chromosome chromStart uint Start position in chromosome chromEnd uint End position in chromosome name string Name of the interaction score uint Score value float Strength of interaction exp string Experiment name color uint Item color sourceChrom string Chromosome of the source interaction region sourceStart uint Start position of the source region sourceEnd uint End position of the source region sourceName string Name for the source region sourceStrand char[1] DNA strand of the source region (+, -, or . for unknown) targetChrom string Chromosome of the target interaction region targetStart uint Start position of the target region targetEnd uint End position of the target region targetName string Name for the target region targetStrand char[1] DNA strand of the target region (+, -, or . for unknown) 2. Example tabix index file: formatted_output_Microglia_PLAC_seq.bed.gz.tbi The annotation track is tabix-indexed to allow efficient retrieval of annotations by chromosome and position. --------------------------------- Generated from: - Metadata: https://tf.lisanwanglab.org/FILER2/metadata/filer2.latest.hg19.template - File schemas: https://tf.lisanwanglab.org/FILER2/metadata/filer2.schemas.latest.tsv - README template: https://tf.lisanwanglab.org/GADB/metadata/filer.dataset.readme.template - Generation date: 06/05/2026