Allele-specific regulatory SNV MPRA in human iPSC-derived cardiomyocytes
Whole genome sequencing delineates regulatory, copy number, and cryptic splice variants in early onset cardiomyopathyA plasmid-based MPRA tested reference and alternative alleles for 46 Tier 1 regulatory SNVs in cardiomyopathy-gene promoters and enhancers. Each allele was represented by at least 25 unique 11-bp barcodes and assayed in five independent biological replicates after transfection into PGP17 human iPSC-derived cardiomyocytes.
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
The library used 135-bp oligonucleotides with the variant centered in the oligo and an 11-bp barcode. The genomic-variant subset contained 2700 oligos, alongside positive and scrambled negative controls in a larger library. The library was transfected into PGP17 iPSC-derived cardiomyocytes with over 80% transfection efficiency, RNA was collected 48 hours later, and tag-seq libraries were sequenced as single-end 50-bp reads on HiSeq 2500. MPRAAnalyze used random oligonucleotides as the null distribution, a likelihood-ratio test, and FDR < 0.05 for significance.
Processed data
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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
- gene_feature_id
- Authors' gene plus regulatory-feature identifier, such as BRAF_P1.
- gene_symbol
- HGNC gene symbol parsed from gene_feature_id.
- regulatory_feature_id
- Promoter or enhancer feature identifier parsed from gene_feature_id, such as P1 or E16.
- chromosome
- Chromosome in the authors' hg19 coordinate system.
- position_hg19
- 1-based variant position in hg19.
- reference_allele
- Reference allele tested in the MPRA oligo.
- alternative_allele
- Alternative allele tested in the MPRA oligo.
- dbsnp
- dbSNP identifier when supplied by the authors; blank when not reported.
- native_status
- Authors' categorical MPRA result: significant effect or no effect.
- p_value
- MPRAAnalyze likelihood-ratio-test p-value for the allele comparison.
- fdr
- Authors' FDR-adjusted p-value.
- log2_fold_change_ref_vs_alt
- Log2 fold change in reporter activity for the reference allele relative to the alternative allele, following the direction shown in Figure 5; positive values indicate higher reference-allele activity and negative values indicate higher alternative-allele activity.
- significant_fdr_0_05
- Boolean indicating FDR < 0.05.
- effect_direction
- Direction derived from log2_fold_change_ref_vs_alt: reference_higher or alternative_higher.
Quality control
The study required at least 25 unique barcodes per allele, used five biological replicates, reported over 80% transfection efficiency across replicates, required RNA integrity number >7 for cDNA synthesis, and excluded cDNA libraries with plasmid contamination by qRT-PCR. Supplementary Figure 5 reports barcode-distribution and replicate-correlation QC. The processed table retains all 46 variants present in the authors' post-analysis Supplementary Table 5; non-significant variants are valid assay results rather than QC failures and are therefore not removed.
Curation notes
This is one MPRA experiment, not the paper's separate luciferase assays, myocardial RNA-seq, or zebrafish experiments. The table is a clean variant-level extraction of Supplementary Table 5 and contains 46 tested regulatory SNVs, including 25 significant results and 15 variants with dbSNP identifiers. The paper does not publicly provide barcode-level DNA/RNA counts or the full 234,500-oligo library; its data-availability statement says additional raw figure data are available from the corresponding author on reasonable request. The source calls the effect column only 'log2 fold change' without stating the numerator. Figure 5's legend/pie and the text's BRAF example support interpreting the reported sign as log2(reference/alternative): negative values indicate higher alternative-allele activity. One prose sentence in the paper instead says 67% had higher reference activity, which conflicts with the plotted legend; this ambiguity is preserved here as a note.