Transcription-factor knockout lentiMPRA during keratinocyte differentiation
Disease-linked regulatory DNA variants and homeostatic transcription factors in epidermisA follow-up trans-factor perturbation MPRA tested the same disease-linked variant library in primary human neonatal foreskin keratinocytes with CRISPR/Cas9 guides targeting IRF6, NRF1, or SNAI2 and an ST26 safe-target control at D0, D3, and D6. The clean table contains variant-level allelic effects, knockout-guide element effects, and guide-by-allele interactions for 3,450 QC-passing groups.
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
CRISPR/Cas9 sgRNA knockout of IRF6, NRF1, or SNAI2; ST26 safe-target control; 1.2 mM calcium-induced differentiation at D0, D3, and D6
The reporter component is an integrated lentiMPRA using Agilent oligos cloned into pGreenFire-mCMV; MPRA activity was measured in cells with TF knockout perturbations and the ST26 safe-target control. Variant-level estimates are from the official MPRAnalyze TFKO sheets; standard errors and omitted omnibus/intercept fields remain available in the raw MOESM3 workbook.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (90 of 90)
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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 · 90 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_allelic_log2_risk_protective
- Official TFKO MPRAnalyze log2 risk-versus-protective activity difference at D0; when risk is unknown, the source uses alternative versus reference.
- d0_allelic_pvalue
- Official TFKO MPRAnalyze p-value for the allelic activity difference at D0.
- d0_allelic_fdr
- Official TFKO MPRAnalyze FDR for the allelic activity difference at D0.
- d0_irf6_effect_log2
- Official TFKO MPRAnalyze log2 effect of the IRF6 knockout guide on reporter-element activity at D0, combining reference and alternative alleles.
- d0_irf6_effect_pvalue
- Official TFKO MPRAnalyze p-value for the IRF6 knockout-guide effect on element activity at D0.
- d0_irf6_effect_fdr
- Official TFKO MPRAnalyze FDR for the IRF6 knockout-guide effect on element activity at D0.
- d0_irf6_allelic_interaction_log2
- Official TFKO MPRAnalyze log2 effect of the IRF6 knockout guide on the risk-versus-protective allelic activity difference at D0.
- d0_irf6_allelic_interaction_pvalue
- Official TFKO MPRAnalyze p-value for the IRF6 guide-by-allele interaction at D0.
- d0_irf6_allelic_interaction_fdr
- Official TFKO MPRAnalyze FDR for the IRF6 guide-by-allele interaction at D0.
- d0_nrf1_effect_log2
- Official TFKO MPRAnalyze log2 effect of the NRF1 knockout guide on reporter-element activity at D0, combining reference and alternative alleles.
- d0_nrf1_effect_pvalue
- Official TFKO MPRAnalyze p-value for the NRF1 knockout-guide effect on element activity at D0.
- d0_nrf1_effect_fdr
- Official TFKO MPRAnalyze FDR for the NRF1 knockout-guide effect on element activity at D0.
- d0_nrf1_allelic_interaction_log2
- Official TFKO MPRAnalyze log2 effect of the NRF1 knockout guide on the risk-versus-protective allelic activity difference at D0.
- d0_nrf1_allelic_interaction_pvalue
- Official TFKO MPRAnalyze p-value for the NRF1 guide-by-allele interaction at D0.
- d0_nrf1_allelic_interaction_fdr
- Official TFKO MPRAnalyze FDR for the NRF1 guide-by-allele interaction at D0.
- d0_snai2_effect_log2
- Official TFKO MPRAnalyze log2 effect of the SNAI2 knockout guide on reporter-element activity at D0, combining reference and alternative alleles.
- d0_snai2_effect_pvalue
- Official TFKO MPRAnalyze p-value for the SNAI2 knockout-guide effect on element activity at D0.
- d0_snai2_effect_fdr
- Official TFKO MPRAnalyze FDR for the SNAI2 knockout-guide effect on element activity at D0.
- d0_snai2_allelic_interaction_log2
- Official TFKO MPRAnalyze log2 effect of the SNAI2 knockout guide on the risk-versus-protective allelic activity difference at D0.
- d0_snai2_allelic_interaction_pvalue
- Official TFKO MPRAnalyze p-value for the SNAI2 guide-by-allele interaction at D0.
- d0_snai2_allelic_interaction_fdr
- Official TFKO MPRAnalyze FDR for the SNAI2 guide-by-allele interaction at D0.
- d3_allelic_log2_risk_protective
- Official TFKO MPRAnalyze log2 risk-versus-protective activity difference at D3; when risk is unknown, the source uses alternative versus reference.
- d3_allelic_pvalue
- Official TFKO MPRAnalyze p-value for the allelic activity difference at D3.
- d3_allelic_fdr
- Official TFKO MPRAnalyze FDR for the allelic activity difference at D3.
- d3_irf6_effect_log2
- Official TFKO MPRAnalyze log2 effect of the IRF6 knockout guide on reporter-element activity at D3, combining reference and alternative alleles.
- d3_irf6_effect_pvalue
- Official TFKO MPRAnalyze p-value for the IRF6 knockout-guide effect on element activity at D3.
- d3_irf6_effect_fdr
- Official TFKO MPRAnalyze FDR for the IRF6 knockout-guide effect on element activity at D3.
- d3_irf6_allelic_interaction_log2
- Official TFKO MPRAnalyze log2 effect of the IRF6 knockout guide on the risk-versus-protective allelic activity difference at D3.
- d3_irf6_allelic_interaction_pvalue
- Official TFKO MPRAnalyze p-value for the IRF6 guide-by-allele interaction at D3.
- d3_irf6_allelic_interaction_fdr
- Official TFKO MPRAnalyze FDR for the IRF6 guide-by-allele interaction at D3.
- d3_nrf1_effect_log2
- Official TFKO MPRAnalyze log2 effect of the NRF1 knockout guide on reporter-element activity at D3, combining reference and alternative alleles.
- d3_nrf1_effect_pvalue
- Official TFKO MPRAnalyze p-value for the NRF1 knockout-guide effect on element activity at D3.
- d3_nrf1_effect_fdr
- Official TFKO MPRAnalyze FDR for the NRF1 knockout-guide effect on element activity at D3.
- d3_nrf1_allelic_interaction_log2
- Official TFKO MPRAnalyze log2 effect of the NRF1 knockout guide on the risk-versus-protective allelic activity difference at D3.
- d3_nrf1_allelic_interaction_pvalue
- Official TFKO MPRAnalyze p-value for the NRF1 guide-by-allele interaction at D3.
- d3_nrf1_allelic_interaction_fdr
- Official TFKO MPRAnalyze FDR for the NRF1 guide-by-allele interaction at D3.
- d3_snai2_effect_log2
- Official TFKO MPRAnalyze log2 effect of the SNAI2 knockout guide on reporter-element activity at D3, combining reference and alternative alleles.
- d3_snai2_effect_pvalue
- Official TFKO MPRAnalyze p-value for the SNAI2 knockout-guide effect on element activity at D3.
- d3_snai2_effect_fdr
- Official TFKO MPRAnalyze FDR for the SNAI2 knockout-guide effect on element activity at D3.
- d3_snai2_allelic_interaction_log2
- Official TFKO MPRAnalyze log2 effect of the SNAI2 knockout guide on the risk-versus-protective allelic activity difference at D3.
- d3_snai2_allelic_interaction_pvalue
- Official TFKO MPRAnalyze p-value for the SNAI2 guide-by-allele interaction at D3.
- d3_snai2_allelic_interaction_fdr
- Official TFKO MPRAnalyze FDR for the SNAI2 guide-by-allele interaction at D3.
- d6_allelic_log2_risk_protective
- Official TFKO MPRAnalyze log2 risk-versus-protective activity difference at D6; when risk is unknown, the source uses alternative versus reference.
- d6_allelic_pvalue
- Official TFKO MPRAnalyze p-value for the allelic activity difference at D6.
- d6_allelic_fdr
- Official TFKO MPRAnalyze FDR for the allelic activity difference at D6.
- d6_irf6_effect_log2
- Official TFKO MPRAnalyze log2 effect of the IRF6 knockout guide on reporter-element activity at D6, combining reference and alternative alleles.
- d6_irf6_effect_pvalue
- Official TFKO MPRAnalyze p-value for the IRF6 knockout-guide effect on element activity at D6.
- d6_irf6_effect_fdr
- Official TFKO MPRAnalyze FDR for the IRF6 knockout-guide effect on element activity at D6.
- d6_irf6_allelic_interaction_log2
- Official TFKO MPRAnalyze log2 effect of the IRF6 knockout guide on the risk-versus-protective allelic activity difference at D6.
- d6_irf6_allelic_interaction_pvalue
- Official TFKO MPRAnalyze p-value for the IRF6 guide-by-allele interaction at D6.
- d6_irf6_allelic_interaction_fdr
- Official TFKO MPRAnalyze FDR for the IRF6 guide-by-allele interaction at D6.
- d6_nrf1_effect_log2
- Official TFKO MPRAnalyze log2 effect of the NRF1 knockout guide on reporter-element activity at D6, combining reference and alternative alleles.
- d6_nrf1_effect_pvalue
- Official TFKO MPRAnalyze p-value for the NRF1 knockout-guide effect on element activity at D6.
- d6_nrf1_effect_fdr
- Official TFKO MPRAnalyze FDR for the NRF1 knockout-guide effect on element activity at D6.
- d6_nrf1_allelic_interaction_log2
- Official TFKO MPRAnalyze log2 effect of the NRF1 knockout guide on the risk-versus-protective allelic activity difference at D6.
- d6_nrf1_allelic_interaction_pvalue
- Official TFKO MPRAnalyze p-value for the NRF1 guide-by-allele interaction at D6.
- d6_nrf1_allelic_interaction_fdr
- Official TFKO MPRAnalyze FDR for the NRF1 guide-by-allele interaction at D6.
- d6_snai2_effect_log2
- Official TFKO MPRAnalyze log2 effect of the SNAI2 knockout guide on reporter-element activity at D6, combining reference and alternative alleles.
- d6_snai2_effect_pvalue
- Official TFKO MPRAnalyze p-value for the SNAI2 knockout-guide effect on element activity at D6.
- d6_snai2_effect_fdr
- Official TFKO MPRAnalyze FDR for the SNAI2 knockout-guide effect on element activity at D6.
- d6_snai2_allelic_interaction_log2
- Official TFKO MPRAnalyze log2 effect of the SNAI2 knockout guide on the risk-versus-protective allelic activity difference at D6.
- d6_snai2_allelic_interaction_pvalue
- Official TFKO MPRAnalyze p-value for the SNAI2 guide-by-allele interaction at D6.
- d6_snai2_allelic_interaction_fdr
- Official TFKO MPRAnalyze FDR for the SNAI2 guide-by-allele interaction at D6.
Quality control
The paper's MPRA QC included complex, non-skewed libraries, observed barcodes, replicate correlation, UMI-tools directional barcode/UMI extraction, Bowtie mapping with one mismatch, and MPRAnalyze 1.9.1. The paper requires at least 5 plasmid-DNA barcodes for both alleles; this package applies that rule to the public pDNA barcode counts, defining detection as >0 count in either pDNA replicate. The official TFKO result sheets and public activity table were retained only for the 3,450 groups passing this rule; no additional statistical cutoff was imposed.
Curation notes
The TFKO series comprises D0/D3/D6 MPRA conditions under NRF1, IRF6, SNAI2, and ST26 safe-target perturbations. The clean table intentionally keeps the one-row-per-variant effect sizes and p/FDR values while omitting standard-error, intercept, and omnibus fields; those full source values are preserved in the raw GSE302354 activity table and MOESM3 workbook. Allelic effects use the source risk-versus-protective orientation, with alternative-versus-reference fallback when risk is unknown.