A CHEQ-seq MPRA tested 190 bp tiles from candidate melanocytic enhancers selected using prior SOX10 knockdown data, in melanoma line MM087. The packaged statistical output compares reporter cDNA with plasmid input for the MPRA library.
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:MM087_patient_derived_melanoma_cell_line
Reference genome
hg19
Design focus
Region-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
The SOX10 knockdown experiment was used to select candidate enhancers for the MPRA library; the MPRA itself was performed in MM087 and does not represent a SOX10-KD versus control MPRA treatment. The table is the author’s DESeq2 condition_cDNA_vs_Plasmid result, including negative controls.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (14 of 14)
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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 · 14 definitions
element_id
Unique 190 bp candidate-enhancer tile identifier from the author DESeq2 output.
parent_region_id
Parent candidate enhancer inferred from the tile identifier.
genomic_coordinates
hg19 tile coordinates parsed from the element identifier where present.
tile_length_bp
Designed tile length in base pairs, generally 190 bp.
design_class
Author-provided sequence class, including Human, Human Rest Topic, and Neg-Control.
negative_control
TRUE when the author class is Neg-Control.
base_mean
DESeq2 mean normalized count across the modeled cDNA/plasmid conditions.
log2_fold_change
DESeq2 log2 fold change for condition_cDNA_vs_Plasmid in the MM087 MPRA; not a knockdown effect size.
lfc_se
Standard error of the DESeq2 log2 fold-change estimate.
stat
DESeq2 test statistic for the cDNA-versus-plasmid contrast.
p_value
Raw DESeq2 p-value for the cDNA-versus-plasmid contrast.
padj
Benjamini-Hochberg adjusted DESeq2 p-value.
fdr_pass
TRUE when padj is below 0.05.
qc_pass
TRUE for rows with finite author statistical output retained after QC.
Quality control
The author output uses DESeq2 on the MM087 cDNA-versus-plasmid comparison after barcode/read filtering and library QC. Rows with finite baseMean, log2 fold change, standard error, test statistic, p-value, and adjusted p-value were retained; the six author-labeled Neg-Control rows were retained for null/background interpretation. FDR pass is padj<0.05.
Curation notes
All 3,404 finite rows in the author-provided DESeq2 table were retained, including six Neg-Control rows. The library name refers to candidate selection by prior SOX10 knockdown data; it should not be interpreted as an MPRA performed under SOX10 knockdown.