SPDEFe(1-200) saturation mutagenesis lentiMPRA
Genomic characterization and therapeutic utilization of IL-13-responsive sequences in asthmaA lentiviral MPRA tested all 600 possible single-nucleotide substitutions across bases 1-200 of the 589-bp SPDEFe enhancer in primary human bronchial epithelial cells from two donors. Cells were cultured at an air-liquid interface with or without IL-13, and the table reports pooled variant effects relative to the wild-type 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.
Perturbation & assay details
Untreated versus 10 ng/mL IL-13 added for the final 7 days of 23-day air-liquid-interface culture
A 230-nt oligo library contained 200-nt test sequences flanked by 15-nt primer-recognition sequences. Inserts were cloned upstream of a minimal promoter driving an eGFP reporter transcript with a barcode in a lentiviral reporter vector; approximately 50 barcodes per sequence were targeted and at least 30 barcodes per sequence were associated for analysis. 250,000 cells from each of two donors were transduced at multiplicity of infection 4, cultured at air-liquid interface for 23 days, and harvested with or without IL-13. MPRAflow associated barcodes and fitted log2 RNA count ~ log2 DNA count + sequence term + intercept; the published log2 variant effect is the pooled comparison against wild type.
Processed data
50 rows per page. Click a cell to inspect its full value.
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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 · 9 definitions
- variant_id
- Stable identifier constructed from SPDEFe, the 1-based position, and the reference>alternative substitution.
- position_1based
- 1-based position within SPDEFe(1-200) reported by Table S10.
- reference_allele
- Reference nucleotide at the tested SPDEFe position.
- alternative_allele
- Single-nucleotide substitution tested against the reference nucleotide.
- dbsnp_id
- dbSNP identifier reported in the source table; blank where Table S10 has no identifier.
- log2_variant_effect
- Published pooled log2 variant effect from the saturation mutagenesis MPRA relative to wild type.
- effect_fold_change
- Derived fold change relative to wild type, calculated as 2^log2_variant_effect.
- fdr
- Published FDR-adjusted p value for the variant effect.
- published_significance_call
- Derived paper-compatible call: increased or decreased when FDR <0.05 and the effect is at least 1.5-fold in either direction; otherwise not_significant.
Quality control
The published MPRAflow workflow filtered barcode associations for NM=0, mapping quality >0, and base quality >30, then required barcode coverage >3 and unique mapping to the enhancer sequence. Two donors were analyzed with at least 30 barcodes per sequence; donor concordance for this saturation library was R=0.77 and the authors pooled the data. P values were FDR-adjusted and enhancer sequences with FDR <0.05 were considered significant. This package retained all 600/600 rows because every source row has valid single-nucleotide alleles and finite effect and FDR values; valid non-significant variants were retained as assay results.
Curation notes
Table S10 exposes the 600 substitution rows only. Although the methods describe a 638-sequence library including wild type and controls, those additional rows are not present in the supplemental workbook and were not fabricated. The paper reports SPDEFe at chr6:34,586,344-34,586,932 in hg38; Table S10 supplies relative positions rather than per-variant genomic coordinates. Blank dbSNP values represent source-missing identifiers.