Experiment / E1FCZKVBEEpisomal Plasmid MPRA

ATAC-seq peak enhancers, CHEQ-seq

Analysis of long and short enhancers in melanoma cell states

An episomal CHEQ-seq MPRA tested selected 501 bp ATAC-seq peak sequences from melanoma cell states in the CHEQ reporter. The processed table reports enhancer-level activity across the seven melanoma cell lines represented in GEO.

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 vector with region-specific barcode assignments; the library contained selected ATAC-seq peak sequences and was measured by plasmid DNA versus reporter cDNA normalization. The eLife supplement supplies designed sequences and construct annotations.

Processed data

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

Visible columns (19 of 19)

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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 · 19 definitions

element_id: Unique ATAC-seq peak/enhancer identifier from GEO.
genomic_coordinates: Broad hg19 coordinate annotation for the ATAC sequence from the eLife library supplement.
element_length_bp: Reported designed sequence length in base pairs.
sequence: Designed ATAC-seq peak sequence from the eLife supplementary library workbook.
enhancer_barcode: Region-specific enhancer barcode listed in the library annotation.
library_generation: Author-provided construct/library generation annotation.
sequence_modification: Author-provided sequence modification or synthesis note.
phenotype: Authors’ phenotype relationship annotation where available.
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 10 assigned barcodes per enhancer, normalized reporter cDNA to plasmid DNA, and used the study’s negative-control/null modeling. Forty-four mapped enhancer rows from the GEO processed file were retained; no row lacked all activity measurements.

Curation notes

The authors describe 46 designed ATAC sequences, with one synthesis failure and 44 sequence IDs represented in the processed GEO table. This table follows the 44 mapped enhancer IDs and joins their sequences/annotations from the supplement where exact IDs were available.

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