The ADSP SNV subset of the combined variation lentiMPRA library was assayed in HEK293FT cells. The processed table reports published bcalm alternate-versus-reference activity effects for the tested single-nucleotide variants.
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:6911
Reference genome
GRCh38
Design focus
Variant-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
The combined variation library used 219 bp oligos centered on ADSP SNVs, matched reference sequences, promoters, and negative controls. Barcode associations used length-specific perfect CIGAR matches, multiple-oligo barcodes were removed, and MPRAsnakeflow counts were analyzed with bcalm in the HEK293FT condition. The table contains the SNV subset and compares alternate sequence to reference sequence.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (18 of 18)
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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 · 18 definitions
variant_id
Source element identifier encoding the tested SNV and genomic allele change.
variant_type
Variant class, SNV.
chromosome
Chromosome reported by the supplementary table.
position_hg38
Variant position reported on hg38/GRCh38.
reference_allele
Reference nucleotide in the source element identifier.
alternate_allele
Alternate nucleotide in the source element identifier.
mutation_descriptor
Reference-to-alternate nucleotide change, formatted as REF>ALT.
log2_fold_change
Published bcalm logFC for alternate versus reference reporter activity.
average_expression
Published average expression value from the model.
t_statistic
Published model t-statistic.
p_value
Published nominal p-value for the alternate-versus-reference effect.
adjusted_p_value
Published multiple-testing-adjusted p-value.
b_statistic
Published limma-style B statistic.
significant_fdr_0_05
Whether adjusted_p_value is at most 0.05.
passes_reported_effect_cutoff
Whether adjusted_p_value is at most 0.05 and absolute log2_fold_change exceeds 0.1, matching the paper’s reported effect criterion.
effect_direction
Direction of alternate activity relative to the reference sequence.
source_table
Supplementary table from which the row was curated.
source_geo_accession
GEO series accession for this MPRA.
Quality control
The authors excluded variants with allele count 0, used length-specific exact barcode mapping, removed barcodes associated with multiple oligos, and analyzed the DNA/RNA counts with bcalm. Package QC retained 8,496 of 8,513 published SNV rows with finite logFC, P.Value, and adj.P.Val values in the [0,1] p-value range; 17 rows with missing model statistics were removed. The reported |logFC| > 0.1 and adjusted-p-value threshold is exposed as a flag but was not used to remove non-significant assay-valid variants.
Curation notes
This child contains the HEK293FT SNV results from the combined variation MPRA; the matched neuronal condition is separate. The supplementary result sheet does not provide dbSNP rs identifiers, so the coordinate-and-allele-bearing source element identifier is retained. Rows with missing bcalm model statistics were excluded, while non-significant but modeled variants remain.