Experiment / E8GLNIVH5Synthetic Regulatory Grammar MPRA

Synthetic SOX-MITF motif combinations

Analysis of long and short enhancers in melanoma cell states

A synthetic regulatory grammar CHEQ-seq MPRA tested combinations of SOX and MITF motifs placed at defined spacings in synthetic backgrounds. The constructs were assayed in melanoma lines MM001, MM074, and MM087, with random-background controls included.

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:MM001_MM074_MM087_patient_derived_melanoma_cell_lines
Reference genome: Not reported / not applicable
Design focus: Synthetic / Motif-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

CHEQ-seq plasmid reporter with synthetic 259 bp backgrounds and SOX/MITF motif combinations at defined spacings; author processed values are CPM-normalized cDNA/plasmid fold changes. Background controls are retained alongside S4/S5 motif-combination constructs.

Processed data

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

Visible columns (13 of 13)

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Page 1 · 50 rows · End of results

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

Column dictionary · 13 definitions

element_id: Unique synthetic construct identifier from the author processed table.
design_class: Author construct class, including S4_combi, S5_combi, and random-sequence trials.
background_control: TRUE for random-background control constructs.
sequence: Synthetic construct sequence from the eLife library supplement when the processed identifier matched exactly.
n_sox_motifs: Number of SOX motif units encoded in the construct name, following the authors’ analysis convention.
n_mitf_motifs: Number of MITF motif units encoded in the construct name, following the authors’ analysis convention.
mm001_activity_fc: CPM-normalized reporter cDNA/plasmid fold-change in melanoma line MM001.
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.
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 Q>30 barcode reads and at least 20 assigned barcodes per synthetic enhancer, normalized reporter cDNA to plasmid input, and used shuffled/background controls for null interpretation. All 50 rows with finite source activity measurements were retained; motif counts follow the authors’ construct-name encoding.

Curation notes

The processed table contains 50 constructs: 24 S4 combinations, 24 S5 combinations, and two random-background trials. Forty-eight sequences joined exactly to the supplement; the two random-trial identifiers did not exactly match the workbook’s background labels, so their sequence cells are blank rather than guessed.

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