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Experiment / E9FE6STC4Integrated lentiMPRA

lentiMPRA of CAD-associated SNP alleles in quiescent 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 were switched to serum-free medium for 24 hours to model the quiescent 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

Serum-free smooth muscle basal medium without FBS for 24 hours (quiescent 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 Quiescent 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 4
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_WithoutFBS and paper term Quiescent are harmonized here. Activity p-values/FDR and author calls come from Supplemental Table 2; allelic results come from Supplemental Table 4. The 209 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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