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Experiment / E4FDC5E6UIntegrated lentiMPRA

lentiMPRA of CAD-associated SNP alleles in proliferative primary human aortic SMCs

Coronary artery disease-associated variants regulate vascular smooth muscle cell gene expression

A 200-bp allele-specific candidate regulatory sequence library was tested after lentiviral integration in primary aortic smooth muscle cells from six donors (three female and three male). Cells remained in complete smooth muscle medium containing 5% FBS for 24 hours to model the proliferative state; RNA/DNA reporter counts were analyzed with MPRAnalyze.

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Organism
Human
Taxonomy ID
NCBITaxon:9606
Biosample
CL:0000359
Reference genome
GRCh38
Design focus
Variant-focused
Region of interest
Not reported / not applicable
Perturbation & assay details

Complete smooth muscle medium containing 5% FBS for 24 hours (proliferative condition); lentiMPRA library transduction at MOI 100

Each CAD-associated SNP was represented by reference and alternate 200-bp sequences centered on the variant, with 15-bp adaptors and randomized molecular barcodes. The constructs were cloned in pLS-SceI, packaged into lentivirus, integrated into primary cells, and read out as RNA/DNA counts after 48 hours; six independent donor cultures were used. MPRAnalyze quantified enhancer activity against scrambled oligos and tested allelic imbalance.

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 · 28 definitions
element_id
Unique designed candidate regulatory sequence identifier, including SNP coordinate and tested allele or control identifier
rs_id
dbSNP rs identifier for a test sequence; control label for negative controls
control_type
Sequence class: test_variant, negative_control, or positive_control
condition
MPRA culture condition, harmonized to the paper's Proliferative label
chromosome
GRCh38 chromosome parsed from the sequence coordinate
start
Interval start coordinate as reported in the GRCh38 coordinate string; no coordinate conversion applied
end
Interval end coordinate as reported in the GRCh38 coordinate string; no coordinate conversion applied
coord_grch38
200-bp GRCh38 CRS interval centered on the tested SNP
reference_allele
Reference allele from Supplemental Table 1
alternate_allele
Alternate allele from Supplemental Table 1
tested_allele
Allele represented by this CRS
allele_role
Whether the tested allele matches the reference or alternate allele in Supplemental Table 1
sequence_200bp
200-bp oligo sequence used in the MPRA
activity_statistic
MPRAnalyze activity statistic reported in Figure 2C source data; blank where that source workbook does not provide a matching value
activity_control_flag
Control indicator carried over from Figure 2C source data
activity_pval_mad
MPRAnalyze MAD-based p-value for enhancer activity versus scrambled controls
activity_fdr
Benjamini-Hochberg FDR for enhancer activity
active_enhancer
Author activity call for the CRS (yes/no)
allelic_log2_fc
Variant-level MPRAnalyze log2 fold-change for the two alleles, repeated on each allele row and reported in Supplemental Table 5
allelic_pval
P-value for the variant-level allelic imbalance test
allelic_fdr
Benjamini-Hochberg FDR for the variant-level allelic imbalance test
allelic_significant_fdr_lt_0_10
Derived yes/no flag for allelic FDR < 0.10
allelic_significant_fdr_le_0_05
Derived yes/no flag for allelic FDR <= 0.05
snp_has_active_allele
Whether the source allelic table marks at least one allele of this SNP as active; repeated on each allele row
stronger_activity_allele
Allele designated as having stronger activity in the source allelic table
weaker_activity_allele
Allele designated as having weaker activity in the source allelic table
qc_min_unique_barcodes
Minimum unique barcode threshold used for inclusion
qc_pass
All rows in this generated table passed the authors' barcode-QC inclusion criterion

Quality control

The authors retained candidate regulatory sequences with at least 10 unique molecular barcodes per CRS; the generated table contains the 40,132 CRS rows present in the authors' barcode-filtered activity output, including barcode-qualified negative controls. MPRAflow counted only barcodes observed in both RNA and DNA for the same sample. MPRAnalyze used scrambled oligos as the negative baseline and Benjamini-Hochberg correction for activity and allelic tests. Statistical-significance flags are preserved from the source outputs; both FDR < 0.10 and FDR <= 0.05 allelic flags are provided because the Results/figure captions and Methods state different thresholds.

Curation notes

Primary cells were isolated from ascending aorta of healthy heart-transplant donors. GEO maps donors C99, G96, and L101 to female and F93, K101, and W87 to male. The source labels SMC_WithFBS and paper term Proliferative are harmonized here. Activity p-values/FDR and author calls come from Supplemental Table 3; allelic results come from Supplemental Table 5. The 236 CRS rows for which Figure 2C lacks a matching activity-statistic entry retain blank activity_statistic values rather than imputation. Some MPRA-tested rs IDs are absent from Supplemental Table 1 and therefore have blank reference/alternate allele annotations.

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