Experiment / E5OUYVD5HIntegrated lentiMPRA

Wild-type allele lentiMPRA during keratinocyte differentiation

Disease-linked regulatory DNA variants and homeostatic transcription factors in epidermis

An integrated lentiviral MPRA tested reference and alternative alleles from the skin-disease regulatory library in primary human neonatal foreskin keratinocytes at D0, D3, and D6. The clean table contains one row per variant group after the reported plasmid-barcode QC, with sequence, regulatory annotation, raw count summaries, and official MPRAnalyze allele-effect statistics.

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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.

Organism: Human
Taxonomy ID: NCBITaxon:9606
Biosample: CL:1001606
Reference genome: GRCh38
Design focus: Variant-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

D0 progenitor conditions; 1.2 mM calcium-induced differentiation for 3 days (D3) or 6 days (D6)

Agilent oligo libraries were cloned into pGreenFire-mCMV (EF1a-puro) and delivered to primary diploid keratinocytes with a lentiviral library. Each library allele was assigned 10 random 16-bp barcodes; reporter RNA barcode counts were processed with UMI-tools directional extraction, Bowtie barcode mapping, and MPRAnalyze 1.9.1.

Processed data

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Column dictionary · 50 definitions

element_id: Unique MPRA variant-group identifier for the tested genomic fragment.
snp_id: Reported rs identifier for the tested variant, when available.
variant_type: Derived allele-class label: SNV, MNV, or indel based on the reference and alternative allele strings.
chromosome: Chromosome of the tested variant.
position_hg38: 1-based GRCh38/hg38 coordinate of the variant.
reference_allele: Reference allele sequence used in the library.
alternative_allele: Alternative allele sequence used in the library.
reference_sequence: Reference genomic insert sequence for the reporter library.
alternative_sequence: Alternative genomic insert sequence for the reporter library.
fragment_start_hg38: Reported GRCh38/hg38 start coordinate of the cloned fragment.
fragment_end_hg38: Reported GRCh38/hg38 end coordinate of the cloned fragment.
reference_fragment_length_bp: Length of the reference insert sequence in base pairs.
alternative_fragment_length_bp: Length of the alternative insert sequence in base pairs.
index_snp: Lead/index GWAS SNP associated with the linked variant.
disease: Skin disease or disease category associated with the index SNP.
risk_alleles: Source risk-allele assignment for the linked disease(s); values such as ref, alt, ?, or comma-separated assignments are retained.
overlapping_genes: Genes overlapping the variant.
nearest_gene: Nearest gene annotation from the source analysis.
distance_to_nearest_gene_bp: Distance from the variant to the nearest gene in base pairs.
eqtl_genes: Genes for which the variant is an eQTL in the source annotation.
loop_genes: Genes whose promoters are linked to the variant by skin HiChIP loops.
promoter_genes: Genes whose promoters overlap the variant.
flipped_ref_alt_to_risk_protective: Whether the source analysis flipped ref/alt orientation so the allelic effect is risk versus protective.
ref_pDNA_barcodes_detected: Number of distinct reference-allele barcode IDs with a count greater than zero in either plasmid-DNA replicate.
alt_pDNA_barcodes_detected: Number of distinct alternative-allele barcode IDs with a count greater than zero in either plasmid-DNA replicate.
ref_pDNA_total_counts: Sum of reference-allele plasmid-DNA counts across both pDNA replicates.
alt_pDNA_total_counts: Sum of alternative-allele plasmid-DNA counts across both pDNA replicates.
d0_ref_RNA_total_counts: Sum of raw reference-allele reporter-RNA barcode counts across D0 replicates.
d0_alt_RNA_total_counts: Sum of raw alternative-allele reporter-RNA barcode counts across D0 replicates.
d3_ref_RNA_total_counts: Sum of raw reference-allele reporter-RNA barcode counts across D3 replicates.
d3_alt_RNA_total_counts: Sum of raw alternative-allele reporter-RNA barcode counts across D3 replicates.
d6_ref_RNA_total_counts: Sum of raw reference-allele reporter-RNA barcode counts across D6 replicates.
d6_alt_RNA_total_counts: Sum of raw alternative-allele reporter-RNA barcode counts across D6 replicates.
d0_log2_risk_protective: Official MPRAnalyze log2 activity difference for risk versus protective alleles at D0; if risk is unknown, the source uses alternative versus reference.
d0_pvalue: Official MPRAnalyze likelihood-ratio-test p-value for the allele difference at D0.
d0_fdr: Official MPRAnalyze FDR for the allele difference at D0.
d0_daSNV: Official source daSNV flag at D0, defined in the supplementary summary as allele-difference FDR < 0.01.
d0_fdr_lt_0_001: Derived boolean indicating the official allele-difference FDR is < 0.001 at D0, the manuscript's primary daSNV cutoff.
d3_log2_risk_protective: Official MPRAnalyze log2 activity difference for risk versus protective alleles at D3; if risk is unknown, the source uses alternative versus reference.
d3_pvalue: Official MPRAnalyze likelihood-ratio-test p-value for the allele difference at D3.
d3_fdr: Official MPRAnalyze FDR for the allele difference at D3.
d3_daSNV: Official source daSNV flag at D3, defined in the supplementary summary as allele-difference FDR < 0.01.
d3_fdr_lt_0_001: Derived boolean indicating the official allele-difference FDR is < 0.001 at D3, the manuscript's primary daSNV cutoff.
d6_log2_risk_protective: Official MPRAnalyze log2 activity difference for risk versus protective alleles at D6; if risk is unknown, the source uses alternative versus reference.
d6_pvalue: Official MPRAnalyze likelihood-ratio-test p-value for the allele difference at D6.
d6_fdr: Official MPRAnalyze FDR for the allele difference at D6.
d6_daSNV: Official source daSNV flag at D6, defined in the supplementary summary as allele-difference FDR < 0.01.
d6_fdr_lt_0_001: Derived boolean indicating the official allele-difference FDR is < 0.001 at D6, the manuscript's primary daSNV cutoff.
is_daSNV_any_timepoint: Official source flag indicating an allele-difference FDR < 0.01 at at least one of D0, D3, or D6.
is_daSNV_fdr_lt_0_001_any_timepoint: Derived boolean indicating an allele-difference FDR < 0.001 at at least one of D0, D3, or D6; 355 rows pass this criterion.

Quality control

The paper reports that the MPRA libraries were complex and not skewed, all barcodes were observed, and biological replicates correlated. UMIs/barcodes were extracted with UMI-tools 1.1.5, barcodes were mapped with Bowtie 1.3.1 allowing one mismatch, and MPRAnalyze 1.9.1 was used for differential activity. Per the paper, SNVs were analyzed only when at least 5 barcodes were detected in plasmid DNA for both reference and alternative alleles; this package defines detection as a barcode with >0 count in either pDNA replicate and retains only groups meeting that rule. The official D0/D3/D6 result sheets contain 3,450 groups after this QC; no additional statistical filtering was applied.

Curation notes

The manuscript abstract reports 3,451 SNVs and 355 daSNVs, while the public library/supplementary tables contain 3,457 variant groups and the official day-level result sheets contain 3,450 groups after barcode QC. The packaged table has 3,450 rows and 355 rows with FDR < 0.001 at any timepoint. Although the paper uses SNV shorthand, the library includes short indels and multibase alleles; variant_type is derived from the source allele strings. Allelic effects retain the source risk-versus-protective orientation and fall back to alternative-versus-reference when risk assignment is ambiguous.

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