A 200-bp Fast SeqProp-designed CRE was tested in SK-N-SH cells with all three alternate nucleotides at each position, producing 600 single-nucleotide substitutions plus the measured parent sequence. The processed table adds the variant's log2FC change relative to the parent sequence.
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
CVCL:0531
Reference genome
Not reported / not applicable
Design focus
Variant-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
The saturation library used the same pMPRAv3:minP-GFP episomal reporter configuration and SK-N-SH MPRA protocol as the CODA library. Each variant ID encodes the reference allele, 1-based position and alternate allele; the activity effect is calculated as variant log2FC minus parent log2FC.
Processed data
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Visible columns (10 of 10)
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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 · 10 definitions
element_id
Publication oligo identifier for the parent or mutated construct.
variant_id
Published allele identifier: m0 for the parent, or m{reference allele}{1-based position}{alternate allele} for a substitution.
reference_allele
Parent nucleotide at the mutated position; empty for the parent row.
position_1based
1-based nucleotide position within the 200-bp parent sequence; empty for the parent row.
alternate_allele
Substituted nucleotide; empty for the parent row.
log2fc
Mean replicate log2 fold-change of reporter expression in SK-N-SH.
log2fc_se
Standard error across replicates for the SK-N-SH log2 fold-change.
parent_log2fc
Measured log2 fold-change of the unmutated parent sequence, repeated for comparison.
delta_log2fc
Variant log2FC minus parent log2FC; the relative mutational activity effect.
cell_type
Cell type in which the saturation-mutagenesis MPRA was performed (SK-N-SH).
Quality control
Applied the publication's replicate-SE reproducibility threshold of lfcSE <= 1 to the complete Supplementary Table 10 records. The source contains 601 rows (m0 parent plus 600 substitutions); mA198T, with lfcSE 3.16073910377719, was excluded, leaving 600 processed rows.
Curation notes
The paper describes all 600 possible single-nucleotide substitutions (three alternatives at each of 200 positions). Supplementary Table 10 additionally includes the parent m0 row. The parent and all retained variants are from a synthetic CRE, so no genomic assembly or continuous genomic region applies.