Experiment / E3TV0E7ISEpisomal Plasmid MPRA

H3K27ac-selected melanoma enhancers, 5′ CHEQ-seq

Analysis of long and short enhancers in melanoma cell states

An episomal CHEQ-seq MPRA tested 5′-configuration reporter constructs containing H3K27ac-selected regions near state-associated melanoma genes. Constructs were assayed across seven patient-derived melanoma cell lines representing melanocytic and mesenchymal-like states.

Download processed table (CSV)Raw source data API documentation

Processed tables are specific to each experiment. Column names, units, measurements, and table structure are not standardized across the database. Check this experiment’s column definitions and quality-control notes before comparing or combining data.

Organism: Human
Taxonomy ID: NCBITaxon:9606
Biosample: UNMAPPED:patient_derived_melanoma_cell_line_panel
Reference genome: hg19
Design focus: Region-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

CHEQ-seq 5′ vector configuration with region-specific random 17 bp barcodes; DNA plasmid and reporter cDNA were measured after transfection. GEO values are the authors’ CPM-normalized cDNA/plasmid fold-change measurements.

Processed data

50 rows per page. Click a cell to inspect its full value.

Visible columns (15 of 15)

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Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.

Column dictionary · 15 definitions

element_id: Unique H3K27ac-selected enhancer identifier from GEO.
genomic_coordinates: Broad hg19 coordinate annotation for the enhancer from the eLife library supplement.
element_length_bp: Reported length of the selected H3K27ac region in base pairs.
phenotype: Authors’ phenotype relationship annotation, such as Invasive or Proliferative.
mm001_activity_fc: CPM-normalized reporter cDNA/plasmid fold-change in melanoma line MM001.
mm057_activity_fc: CPM-normalized reporter cDNA/plasmid fold-change in melanoma line MM057.
mm074_activity_fc: CPM-normalized reporter cDNA/plasmid fold-change in melanoma line MM074.
mm087_activity_fc: CPM-normalized reporter cDNA/plasmid fold-change in melanoma line MM087.
mm029_activity_fc: CPM-normalized reporter cDNA/plasmid fold-change in melanoma line MM029.
mm047_activity_fc: CPM-normalized reporter cDNA/plasmid fold-change in melanoma line MM047.
mm099_activity_fc: CPM-normalized reporter cDNA/plasmid fold-change in melanoma line MM099.
n_measured_lines: Number of melanoma lines with a finite activity measurement.
mean_activity_fc: Arithmetic mean of the available per-line activity fold changes; derived during packaging.
log2_mean_activity_fc: Base-2 logarithm of mean_activity_fc; derived during packaging.
qc_pass: TRUE for rows retained after source-table and finite-measurement QC.

Quality control

Author processing required barcode sequencing quality Q>30 and at least 5 assigned barcodes per enhancer, normalized reporter cDNA to plasmid DNA, and used shuffled/negative controls with a Gaussian null and Benjamini-Hochberg significance testing. The processed GEO table was retained at the enhancer level; rows with valid measurements were kept and missing line-specific values remain blank.

Curation notes

The processed source table contains 38 enhancers. MAP3K14_1 had a missing GEO phenotype label and was filled from the eLife supplement; sparse but finite enhancer measurements were retained rather than imputed. Element identifiers follow the author/GEO nomenclature.

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