Experiment / E4RO0XIMKEpisomal Plasmid MPRA

C283T immortalized melanocyte episomal allelic MPRA

Massively parallel reporter assays and variant scoring identified functional variants and target genes for melanoma loci and highlighted cell-type specificity

The 191,232-oligo library tested 1,992 melanoma-GWAS variants as 145-bp reference and alternative sequences in both orientations with barcode tags. The library was transfected into the C283T human immortalized melanocyte line in 5 biological transfections, normalized to MPRA DNA Inputs 2 or 3.

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Organism: Human
Taxonomy ID: NCBITaxon:9606
Biosample: UNMAPPED:C283T
Reference genome: hg19
Design focus: Variant-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated; harvested 24 h after transfection

Episomal pMPRA1/pMPRAdonor2 luc2 reporter with a minimal promoter; each allele was represented by forward and reverse-complement 145-bp test sequences and 20 12-bp random barcode tags per unique sequence (with a 2-bp AC spacer). C283T cells were electroporated with the Lonza P2 Primary Cell 4D-Nucleofector X Kit in 5 biological transfections; T1 used DNA Input 2 and T2-T5 used DNA Input 3.

Processed data

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Column dictionary · 41 definitions

variant_id: Variant identifier as chromosome:position on hg19; multiallelic variants use the S2 A/B suffix.
rsid: dbSNP rs identifier, or NA for variants without an rs identifier.
gwas_locus: Melanoma GWAS locus label assigned by the authors.
ref_allele: Reference allele used in the MPRA oligo.
alt_allele: Alternative allele used in the MPRA oligo.
ref_sequence_145bp: 145-bp forward-strand reference test sequence from Table S3.
alt_sequence_145bp: 145-bp forward-strand alternative test sequence from Table S3.
n_qc_tags: Number of unique reference plus alternative barcode tags with DNA TPM >=2 in at least one input library used for this experiment.
n_ref_qc_tags: Unique reference-allele barcode tags passing the DNA TPM >=2 filter.
n_alt_qc_tags: Unique alternative-allele barcode tags passing the DNA TPM >=2 filter.
n_qc_observations: Number of allele-tag by transfection observations retained after DNA TPM QC; RNA-nondetected tags are represented as zero TPM.
n_ref_qc_observations: Reference-allele tag by transfection observations passing DNA TPM QC.
n_alt_qc_observations: Alternative-allele tag by transfection observations passing DNA TPM QC.
n_ref_rna_detected_observations: QC-passing reference observations with a detected RNA tag in the deposited RNA count table.
n_alt_rna_detected_observations: QC-passing alternative observations with a detected RNA tag in the deposited RNA count table.
mean_ref_log2_rna_dna: Mean log2((RNA TPM + 1)/(DNA TPM + 1)) across QC-passing reference observations.
mean_alt_log2_rna_dna: Mean log2((RNA TPM + 1)/(DNA TPM + 1)) across QC-passing alternative observations.
raw_log2_fc_alt: Raw-derived alternative-minus-reference difference between the two mean log2 RNA/DNA ratios.
author_log2_fc_alt: Authors' reported log2 fold difference for alternative versus reference allelic activity from the current MPRA regression (Table S6 or S7).
author_fdr: Authors' BH-adjusted FDR for the current MPRA allelic regression (Table S6 or S7); 0 is reported as 0 in the source workbook.
author_mtsa_log2_fc_alt: Authors' MTSA-corrected log2 fold difference for alternative versus reference allelic activity (Table S8).
author_mtsa_fdr: Authors' MTSA-corrected BH-adjusted FDR (Table S8).
author_mpra_significant: Y when the authors' current-MPRA FDR is <0.01; otherwise N or NA.
ref_effect: Authors' melanoma-risk/protective classification of the reference allele.
risk_direction: Authors' direction of the melanoma-risk allele relative to the protective allele in this MPRA.
activator: Authors' putative activator/repressor annotation from MPRA activity inference (Table S12).
open_chromatin_annotation: Authors' number/category of open-chromatin datasets overlapping the variant (Table S12).
histone_annotation: Authors' enhancer/promoter histone annotation (Table S12).
motif_sig_count: Number of significant motifBreakR predictions for the variant (Table S12).
motif_strong_count: Number of strong motifBreakR effects for the variant (Table S12).
integrative_score: Authors' combined variant-prioritization score across MPRA, chromatin, motif, and fine-mapping features (Table S12).
tier: Authors' within-locus prioritization tier (Table S12).
prioritized: Y when the authors prioritized the variant based on Tier 1 or Tier 2 (Table S12).
SKCM_eGenes: Semicolon-separated significant eGenes linked in the TCGA skin cutaneous melanoma QTL dataset.
melanocyte_eGenes: Semicolon-separated significant eGenes linked in the primary melanocyte QTL dataset.
SKCM_meGenes: Semicolon-separated significant meGenes linked in the TCGA skin cutaneous melanoma methylation-QTL dataset.
melanocyte_meGenes: Semicolon-separated significant meGenes linked in the primary melanocyte methylation-QTL dataset.
cell_type_specific: Authors' cell-type-specific designation for this experiment; NA means it was not in the corresponding S16/S17 subset.
cell_type_score: Authors' corresponding cell-type specificity score from S16 or S17.
cell_type_fdr: Authors' FDR for the allelic-effect by cell-type interaction from S16 or S17.
cell_type_TFs: Authors' transcription factors predicted to explain the corresponding cell-type specificity.

Quality control

The authors reported high recovery and replicate reproducibility in Table S4. For this package (C283T immortalized melanocyte; 5 transfections.), each GEO barcode TPM table was joined to Table S3, and the authors' normalization log2((RNA TPM + 1)/(DNA TPM + 1)) was calculated using the input assignment recorded in GEO. Barcode observations with DNA input TPM <2 were removed as specified in the paper; RNA tags absent from a deposited RNA table were treated as zero TPM after the pseudocount. Scrambled control oligos were excluded from the variant table. Variants without at least one QC-passing reference and alternative observation were excluded (17 excluded; 1975 retained). The table retains all QC-passing tested variants, not only significant hits; author MPRA significance is FDR <0.01. Author FDR/effect fields are copied from Table S6/S7 and MTSA-corrected fields from Table S8.

Curation notes

Raw-derived mean ratios use all input-qualified mapped reference/alternative tag observations, with missing RNA tags represented by zero TPM; the simple raw mean is expected to differ from the authors’ strand- and transfection-adjusted robust regression coefficient. For validation, the mean absolute difference between raw-derived and author log2 effects for variants with both values was 0.0143. C283T is described by GEO and the paper as an immortalized melanocyte line, but no Cellosaurus accession was found during resolution, so UNMAPPED:C283T is used.

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