Experiment / E6WE06IIQStandard STARR-seq

ATAC-seq peak enhancers, STARR-seq

Analysis of long and short enhancers in melanoma cell states

A standard episomal STARR-seq assay tested the selected 501 bp ATAC-seq peak sequences in a self-transcribing reporter configuration. 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

Episomal STARR-seq ORI reporter configuration using the same selected ATAC-seq peak sequence set as the CHEQ-seq comparison. Activity is based on author-provided CPM-normalized reporter RNA/plasmid fold-change values.

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 shared ATAC 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 STARR-seq reporter RNA/plasmid fold-change in melanoma line MM001.
mm057_activity_fc: CPM-normalized STARR-seq reporter RNA/plasmid fold-change in melanoma line MM057.
mm074_activity_fc: CPM-normalized STARR-seq reporter RNA/plasmid fold-change in melanoma line MM074.
mm087_activity_fc: CPM-normalized STARR-seq reporter RNA/plasmid fold-change in melanoma line MM087.
mm029_activity_fc: CPM-normalized STARR-seq reporter RNA/plasmid fold-change in melanoma line MM029.
mm047_activity_fc: CPM-normalized STARR-seq reporter RNA/plasmid fold-change in melanoma line MM047.
mm099_activity_fc: CPM-normalized STARR-seq reporter RNA/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 for the selected ATAC library, normalized reporter signal to plasmid input, and applied the study’s null-control modeling. Forty-four mapped enhancer rows from the GEO processed file were retained; no row lacked all activity measurements.

Curation notes

This is the paper’s orthogonal STARR-seq comparison for the ATAC library, not an additional CHEQ-seq replicate. It contains 44 mapped enhancer rows and shares library sequence annotations with the CHEQ-seq ATAC experiment.

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