50-variant episomal MPRA in paired lymphoblastoid cell lines
Three linked variants have opposing regulatory effects on isovaleryl-CoA dehydrogenase gene expressionA 50-construct allele-focused MPRA library centered 180 bp of native sequence around candidate IVD variants and was assayed in NA12878 and NA19239 lymphoblastoid cell lines. This package uses the authors' combined-LCL Table S4 summary, including reference/alternative RNA-versus-plasmid activity and allele-skew measurements.
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
Basal / Untreated
Agilent oligos centered 180-bp regions around each tested allele, with 15-bp flanking adapters. Unique 20-bp adapter sequences were added by emulsion PCR, and a constant region enabled Gibson assembly. The final episomal construct placed a minimal promoter and GFP between the test sequence and the unique adapter so the adapter was transcribed in the 3' GFP transcript. Oligo-adapter associations were measured with 2 x 150-bp HiSeq reads; reporter and plasmid adapter counts were obtained by 1 x 30-bp HiSeq sequencing. The library was electroporated into NA12878 in five sequential-day replicates and NA19239 in three replicates. The packaged Table S4 is the combined LCL analysis.
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 · 29 definitions
- element_id
- Unique construct identifier from Supplementary Table S4.
- centered_variant
- Centered variant identifier from Table S4, including the chr15 indel notation used by the source.
- functional_label
- Article label for the four named loci: alpha, beta, delta, or tau; blank for other tested variants.
- chromosome
- Chromosome reported in Supplementary Table S2.
- position_hg19
- Variant position on hg19 reported in Supplementary Table S2.
- associated_gene
- Ensembl gene identifier associated with the Table S2 eQTL record; here ENSG00000128928 is IVD.
- direction_relative_to_tss
- Source strand/orientation label for the oligo relative to the IVD transcription start site.
- allele_context
- Source Haplotype field: ref or alt surrounding sequence background; it is not an explicit nucleotide allele call.
- reference_plasmid_mean
- Normalized starting-plasmid count mean for the reference-allele construct.
- reference_rna_mean
- Reporter RNA count mean for the reference-allele construct.
- reference_log2fc
- Source reference-construct log2 fold change of RNA relative to plasmid DNA.
- reference_neg_log10_p
- Negative log10 of the source reference-construct expression p-value (Table S4 C.A.logP).
- reference_neg_log10_bh_p
- Negative log10 of the source BH-adjusted reference-construct expression p-value (Table S4 C.A.logPadj).
- alternative_plasmid_mean
- Normalized starting-plasmid count mean for the alternative-allele construct.
- alternative_rna_mean
- Reporter RNA count mean for the alternative-allele construct.
- alternative_log2fc
- Source alternative-construct log2 fold change of RNA relative to plasmid DNA.
- alternative_neg_log10_p
- Negative log10 of the source alternative-construct expression p-value (Table S4 C.B.logP).
- alternative_neg_log10_bh_p
- Negative log10 of the source BH-adjusted alternative-construct expression p-value (Table S4 C.B.logPadj).
- log2_skew_na12878
- Alternative-versus-reference log2 allelic skew measured in NA12878.
- log2_skew_na19239
- Alternative-versus-reference log2 allelic skew measured in NA19239.
- log2_skew_combined
- Alternative-versus-reference log2 allelic skew from the combined LCL analysis.
- skew_neg_log10_bh_p_na12878
- Negative log10 of the NA12878 BH-adjusted skew statistic from Table S4 Skew.fdr.12878.
- skew_neg_log10_bh_p_na19239
- Negative log10 of the NA19239 BH-adjusted skew statistic from Table S4 Skew.fdr.19239.
- skew_neg_log10_p_combined
- Negative log10 of the combined-LCL allelic-skew p-value (Table S4 C.Skew.logP).
- skew_neg_log10_bh_p_combined
- Negative log10 of the combined-LCL BH-adjusted allelic-skew p-value (Table S4 C.Skew.fdr).
- reference_active_fdr_0_05
- Boolean derived from reference_neg_log10_bh_p >= -log10(0.05).
- alternative_active_fdr_0_05
- Boolean derived from alternative_neg_log10_bh_p >= -log10(0.05).
- allelic_skew_fdr_0_05
- Boolean derived from skew_neg_log10_bh_p_combined >= -log10(0.05).
- source_excel_row
- Original workbook row number in Table S4.
Quality control
The authors applied Benjamini-Hochberg correction and used FDR < 0.05 as the MPRA significance threshold. Package QC retained 49 of 50 Table S4 construct rows after requiring finite normalized plasmid and RNA means of at least 10 for both reference and alternative constructs; rs8040086_A (source workbook row 56) was excluded because all four coverage means were below 10. Nonsignificant, adequately covered constructs were retained as informative negative results. Source NA values are blank in the processed CSV but are preserved in raw_data.
Curation notes
The two biological cell lines are GM12878/NA12878 (Cellosaurus CVCL:7526) and GM19239/NA19239 (Cellosaurus CVCL:9634), so biosample_id is null for this combined-LCL table. The article reports five NA12878 and three NA19239 transfections. The article's named functional variants are rs111540938 (alpha), rs10851395 (beta), rs66791338 (delta; represented in Table S4 as chr15:40714431:D), and rs11638033 (tau). The paper alternates rs11633883 and rs11638033 in a nearby indel description; both source identifiers are retained without silent correction, while tau is assigned only to rs11638033 based on the main text and Table S2. The second, deletion-tiling MPRA around delta is documented in the raw supplementary PDF but has no accessible numeric result table, so it is not represented by fabricated rows or a separate child experiment.