README file for the VISTA_enhancer_transgenic_enhancer_bed11_hg19 dataset I. Description of the dataset -------------------------------- Data source: VISTA_Enhancer Data source URL: https://enhancer.lbl.gov/ Genome build: hg19 File format: bed bed6+5 VISTA_enhancer, bgzip-compressed and tabix-indexed Contents: Transgenic mouse assay transcriptional enhancers validated in transgenic mouse assay Dataset URL: https://tf.lisanwanglab.org/GADB/FILER2/Annotationtracks/VISTA_enhancer/transgenic_enhancer/bed11/hg19/ Acknowledgements: https://tf.lisanwanglab.org/GADB/FILER2/acknowledgements/VISTA_Enhancer.html II. Dataset version number -------------------------------- v2_0529_2026 III. Files in the dataset -------------------------------- See MANIFEST for the complete file list. Summary: - Files: 22 *.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 https://enhancer.lbl.gov/. VII. File Contents -------------------------------- 1. Example annotation file: Trigeminal_v_ganglion_cranial.VISTA_Human_enhancers_sequences.bed.gz File schema: fieldName sqlType fieldDescription chrom string Reference sequence chromosome chromStart uint Start position in chromosome, 0-based coordinate system chromEnd uint End position in chromosome name string Identifier for the experiment score float Score strand char[1] Strand (+ for forward, - for reverse) annotation string Annotation of the enhancer activity. POSITIVE if reproducible expression was observed in transgenic embryos and NEGATIVE if no reproducible expression was observed enhancer_sequence lstring Sequence of the enhancer region reference_sequence lstring Reference sequence for the enhancer region expressionPattern string Anatomical region and frequency of enhancer activity in embryos. e.g., forebrain[9/11] Flanking_genes string Names of genes flanking the enhancer region 2. Example tabix index file: Trigeminal_v_ganglion_cranial.VISTA_Human_enhancers_sequences.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