QT interval GWAS enhancer-variant MPRA in HL-1 cardiomyocytes
Massively parallel reporter assays identify functional enhancer variants at QT interval GWAS lociAn episomal pGL4.23/eGFP MPRA tested 200-mer oligos containing 129-bp human genomic sequences centered on 1,018 biallelic QT-interval GWAS variants, with reference and alternate alleles each assigned 50 unique barcodes. The same screen used two plasmid-library propagation versions (V1, Stable cells; V2, DH10beta cells) and two oligo pools, with three DNA input replicates and ten HL-1 RNA replicates per version and pool.
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
Variant-centered enhancer oligos were cloned into a pGL4.23-derived episomal backbone, followed by insertion of the minimal-promoter eGFP reporter cassette, and transfected with FuGENE HD into mouse HL-1 cardiomyocytes. V1 and V2 differ in the E. coli host used to propagate the pGL4.23 library (Stable and DH10beta, respectively); the biological reporter condition is otherwise the same. Barcode sequencing measured three plasmid-DNA input replicates and ten post-transfection mRNA replicates per pool and version.
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 · 56 definitions
- variant_id
- Variant identifier, usually an rsID.
- variant_class
- SNV when both alleles are one base; otherwise INDEL.
- chromosome
- Chromosome label for the tested human variant.
- position_hg19
- Published 1-based hg19 coordinate from Data S4.
- position_grch38
- Published 1-based GRCh38/hg38 coordinate from Data S4.
- reference_allele
- Reference allele tested in the MPRA.
- alternate_allele
- Alternate allele tested in the MPRA.
- pool
- Oligo pool number (1 or 2).
- locus
- Published QTi GWAS locus or associated gene label.
- gene_id
- Published Ensembl gene identifier associated with the locus.
- ref_test_element_129bp
- 129-bp reference-allele test element extracted from the designed 200-mer oligo.
- alt_test_element_129bp
- 129-bp alternate-allele test element extracted from the designed 200-mer oligo.
- oligos_per_allele_designed
- Number of designed barcoded oligos per allele (50).
- v1_dna_ref_count
- V1 aggregate reference-allele DNA barcode count summed across three DNA replicates.
- v1_dna_alt_count
- V1 aggregate alternate-allele DNA barcode count summed across three DNA replicates.
- v1_dna_ref_cpm
- V1 reference-allele DNA count per million, normalized within the matching pool.
- v1_dna_alt_cpm
- V1 alternate-allele DNA count per million, normalized within the matching pool.
- v1_ref_barcodes_with_dna
- V1 designed reference barcodes with a nonzero aggregate DNA count.
- v1_alt_barcodes_with_dna
- V1 designed alternate barcodes with a nonzero aggregate DNA count.
- v1_rna_ref_count
- V1 aggregate reference-allele RNA barcode count across valid RNA replicates.
- v1_rna_alt_count
- V1 aggregate alternate-allele RNA barcode count across valid RNA replicates.
- v1_rna_ref_cpm
- V1 reference-allele RNA count per million, normalized within valid RNA replicates of the matching pool.
- v1_rna_alt_cpm
- V1 alternate-allele RNA count per million, normalized within valid RNA replicates of the matching pool.
- v1_ref_log2_rna_dna
- V1 descriptive log2 ratio of normalized reference RNA CPM to reference DNA CPM; blank when undefined.
- v1_alt_log2_rna_dna
- V1 descriptive log2 ratio of normalized alternate RNA CPM to alternate DNA CPM; blank when undefined.
- v1_allelic_log2fc_from_counts
- V1 descriptive alternate-minus-reference difference of the count-derived log2 RNA/DNA activities.
- v1_rna_replicates_used
- Number of V1 RNA replicates used for the count-derived summaries (10, or 9 for Pool 2 after the paper's exclusion).
- v2_dna_ref_count
- V2 aggregate reference-allele DNA barcode count summed across three DNA replicates.
- v2_dna_alt_count
- V2 aggregate alternate-allele DNA barcode count summed across three DNA replicates.
- v2_dna_ref_cpm
- V2 reference-allele DNA count per million, normalized within the matching pool.
- v2_dna_alt_cpm
- V2 alternate-allele DNA count per million, normalized within the matching pool.
- v2_ref_barcodes_with_dna
- V2 designed reference barcodes with a nonzero aggregate DNA count.
- v2_alt_barcodes_with_dna
- V2 designed alternate barcodes with a nonzero aggregate DNA count.
- v2_rna_ref_count
- V2 aggregate reference-allele RNA barcode count across valid RNA replicates.
- v2_rna_alt_count
- V2 aggregate alternate-allele RNA barcode count across valid RNA replicates.
- v2_rna_ref_cpm
- V2 reference-allele RNA count per million, normalized within valid RNA replicates of the matching pool.
- v2_rna_alt_cpm
- V2 alternate-allele RNA count per million, normalized within valid RNA replicates of the matching pool.
- v2_ref_log2_rna_dna
- V2 descriptive log2 ratio of normalized reference RNA CPM to reference DNA CPM; blank when undefined.
- v2_alt_log2_rna_dna
- V2 descriptive log2 ratio of normalized alternate RNA CPM to alternate DNA CPM; blank when undefined.
- v2_allelic_log2fc_from_counts
- V2 descriptive alternate-minus-reference difference of the count-derived log2 RNA/DNA activities.
- v2_rna_replicates_used
- Number of V2 RNA replicates used for the count-derived summaries (10, or 9 for Pool 2 after the paper's exclusion).
- mean_allelic_log2fc_from_counts
- Arithmetic mean of the available V1 and V2 count-derived allelic log2 fold changes.
- qc_pass
- Boolean indicating the published combined DNA-CPM QC passed; all rows in this filtered table are true.
- is_enhancer
- Published indicator that at least one allele showed enhancer activity.
- is_allelic
- Published indicator of a significant allelic activity difference under the paper's criteria.
- published_alpha_ref
- Published MPRAnalyze reference-allele transcription-rate alpha.
- published_alpha_alt
- Published MPRAnalyze alternate-allele transcription-rate alpha.
- published_log2a_ref
- Published log2-transformed reference-allele activity value.
- published_log2a_alt
- Published log2-transformed alternate-allele activity value.
- published_zscore_ref
- Published reference-allele activity Z-score.
- published_zscore_alt
- Published alternate-allele activity Z-score.
- published_logFC_alt_vs_ref
- Published MPRAnalyze alternate-versus-reference log fold change.
- published_pval_allelic
- Published likelihood-ratio-test p-value for the allelic comparison.
- published_fdr_allelic
- Published Benjamini-Hochberg FDR for the allelic comparison.
- published_deltaSVM
- Published deltaSVM sequence-based predicted allele effect.
- luciferase_only
- Published indicator that the variant was marked luciferase-only in Data S4.
Quality control
The paper assessed oligo representation, allele representation, synthesis errors, barcode reproducibility, and barcode sequence effects. It used only perfect barcode matches, excluded variants with less than 8 CPM for either allele in the plasmid-DNA libraries, excluded V1 Pool 2 RNA replicate 2 and V2 Pool 2 RNA replicate 7 from downstream activity modeling because of weaker replicate correlation, and analyzed V1 and V2 together with MPRAnalyze. The published combined QC retained 938 of 1,018 variants. The package retains exactly the 938 rows with Data S4 DNA_CPM_QC=TRUE, verifies that raw GEO DNA aggregates reproduce the published count and CPM fields (maximum CPM difference approximately 5e-12), and applies no additional row exclusions. Count-derived RNA summaries use the remaining 10 RNA replicates except for the two paper-excluded libraries, which use 9.
Curation notes
This package represents one MPRA experiment with two library versions and two oligo pools; V1 and V2 are propagation/library versions rather than distinct HL-1 biological conditions. The processed table is variant-level, while the raw GEO matrices retain barcode-level DNA and RNA counts. Data S1 contains 200 additional Empty control oligos; those controls are retained in raw_data but excluded from the 1,018-variant sequence map. Missing values originally encoded as NA in Data S4 are blank in table.csv. The published statistics are carried through under published_* columns. The *_from_counts columns are transparent descriptive summaries calculated from GEO counts and are not replacements for the paper's MPRAnalyze model. HL-1 was resolved to Cellosaurus CVCL:0303, a transformed mouse cardiomyocyte line.